5w5y - Revision history

OCA at 22:17, 10 April 2020

OCA — Fri, 10 Apr 2020 22:17:53 GMT

←Older revision		Revision as of 22:17, 10 April 2020
Line 3:		Line 3:
	<SX load='5w5y' size='340' side='right' viewer='molstar' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='5w5y' size='340' side='right' viewer='molstar' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRN6, YBL014C, YBL0311, YBL0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN7, YJL025W, J1273 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN11, YML043C, YM9827.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRN6, YBL014C, YBL0311, YBL0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN7, YJL025W, J1273 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN11, YML043C, YM9827.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5w5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5y OCA], [http://pdbe.org/5w5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5y RCSB], [http://www.ebi.ac.uk/pdbsum/5w5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5y ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5w5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5y OCA], [http://pdbe.org/5w5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5y RCSB], [http://www.ebi.ac.uk/pdbsum/5w5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5y ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 19:55, 6 March 2020

OCA — Fri, 06 Mar 2020 19:55:30 GMT

←Older revision		Revision as of 19:55, 6 March 2020
Line 1:		Line 1:

	==RNA polymerase I Initial Transcribing Complex==		==RNA polymerase I Initial Transcribing Complex==
-	<~~StructureSection~~ load='5w5y' size='340' side='right'caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='5w5y' size='340' side='right' viewer='molstar' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>
Line 11:		Line 11:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~RPAC2_YEAST RPAC2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common ~~core~~ component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/~~RPA43_YEAST RPA43_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Component~~ of RNA ~~polymerase~~ I which ~~synthesizes~~ ribosomal RNA precursors~~. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro~~, ~~the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts~~ as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, ~~CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex~~.~~<ref>PMID:8887672</ref>~~ [[http://www.uniprot.org/uniprot/~~RPA2_YEAST RPA2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Second largest core~~ component of RNA ~~polymerase~~ I which ~~synthesizes~~ ribosomal RNA precursors~~. Proposed to contribute to the polymerase catalytic activity~~ and ~~forms the polymerase active center together with the largest subunit~~. ~~Pol I is composed of mobile elements and RPA2~~ is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RPA1_YEAST RPA1_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Largest and catalytic core component~~ of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~Forms the polymerase active center together~~ with ~~the second largest subunit. A single stranded DNA template strand of the promoter~~ is ~~positioned within the central active site cleft~~ of Pol I~~. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought~~ to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters ~~and plays a role in Pol I recruitment~~. ~~After binding of UAF (upstream activation factor) to an upstream element of~~ the ~~promoter, CF is recruited in a SPT15/TBP~~-~~dependent manner to form a pre~~-~~initiation complex~~.<ref>PMID:~~21921198~~</ref> <ref>PMID:~~21940764</ref> <ref>PMID:8887672~~</ref> [[http://www.uniprot.org/uniprot/~~RPA49_YEAST RPA49_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired~~ transcriptional ~~activity and increased sensitivity to alpha-amanitin~~. ~~The function~~ of ~~A49 might be linked~~ to ~~the RNase H activity that was found associated with this subunit~~. [[http://www.uniprot.org/uniprot/~~RPAB2_YEAST RPAB2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Common~~ component of RNA ~~polymerases~~ I~~, II and III~~ which ~~synthesize~~ ribosomal RNA precursors~~, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively~~. ~~Pol II is~~ the ~~central component of the basal RNA~~ polymerase ~~II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element~~ and ~~togther with parts of RPB1 and RPB2~~ forms ~~a pocket to which~~ the ~~RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA~~ polymerase ~~catalyzes~~ the ~~transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates~~. ~~Common component~~ of ~~RNA polymerases I~~ and ~~III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1~~ is part of the ~~Pol~~ core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RPA12_YEAST RPA12_YEAST~~]] ~~DNA-dependent RNA polymerase catalyzes the transcription~~ of ~~DNA into RNA using~~ the ~~four ribonucleoside triphosphates as substrates. Component~~ of RNA polymerase I ~~which synthesizes ribosomal RNA precursors~~. ~~Involved in transcriptional termination. Involved in recruitment~~ of ~~RPA49~~ to ~~Pol I~~.<ref>PMID:~~15073335~~</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).	+	[[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC2_YEAST RPAC2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA43_YEAST RPA43_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro, the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA12_YEAST RPA12_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Involved in transcriptional termination. Involved in recruitment of RPA49 to Pol I.<ref>PMID:15073335</ref> [[http://www.uniprot.org/uniprot/RPA2_YEAST RPA2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]

OCA at 08:09, 27 November 2019

OCA — Wed, 27 Nov 2019 08:09:12 GMT

←Older revision		Revision as of 08:09, 27 November 2019
Line 1:		Line 1:

	==RNA polymerase I Initial Transcribing Complex==		==RNA polymerase I Initial Transcribing Complex==
-	<StructureSection load='5w5y' size='340' side='right' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='5w5y' size='340' side='right'caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5w5y" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w5y" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 30:
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Han, Y]]		[[Category: Han, Y]]
	[[Category: He, Y]]		[[Category: He, Y]]
	[[Category: Rna polymerase i core factor transcription]]		[[Category: Rna polymerase i core factor transcription]]
	[[Category: Transcription]]		[[Category: Transcription]]

OCA at 09:29, 18 July 2018

OCA — Wed, 18 Jul 2018 09:29:14 GMT

←Older revision		Revision as of 09:29, 18 July 2018
Line 11:		Line 11:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~RPAB2_YEAST RPAB2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I~~, II~~ and III which synthesize ribosomal RNA ~~precursors, mRNA~~ precursors ~~and many functional non-coding RNAs,~~ and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/~~RPAC2_YEAST RPAC2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Common core component~~ of RNA ~~polymerases~~ I ~~and III~~ which ~~synthesize~~ ribosomal RNA precursors ~~and small RNAs~~, ~~such~~ as ~~5S rRNA and tRNAs~~, ~~respectively~~. [[http://www.uniprot.org/uniprot/~~RPAC1_YEAST RPAC1_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Common~~ component of RNA ~~polymerases~~ I ~~and III~~ which ~~synthesize~~ ribosomal RNA precursors and ~~small RNAs, such as 5S rRNA and tRNAs, respectively~~. ~~RPAC1~~ is part of the ~~Pol~~ core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RPA43_YEAST RPA43_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Component~~ of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~Through its association~~ with ~~RRN3~~ is ~~involved in recruitment~~ of Pol I to rDNA promoters. ~~In vitro,~~ the ~~A13~~-~~A43 subcomplex binds single~~-~~stranded RNA~~.<ref>PMID:~~11032814~~</ref> <ref>PMID:~~12888498~~</ref> [[http://www.uniprot.org/uniprot/~~RPA12_YEAST RPA12_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~Involved in~~ transcriptional ~~termination~~. ~~Involved in recruitment~~ of ~~RPA49~~ to ~~Pol I~~.~~<ref>PMID:15073335</ref>~~ [[http://www.uniprot.org/uniprot/~~RPA2_YEAST RPA2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Second largest core~~ component of RNA ~~polymerase~~ I which ~~synthesizes~~ ribosomal RNA precursors. ~~Proposed to contribute to~~ the polymerase ~~catalytic activity~~ and forms the polymerase ~~active center together with~~ the ~~largest subunit~~. ~~Pol I is composed~~ of ~~mobile elements~~ and ~~RPA2~~ is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RRN11_YEAST RRN11_YEAST~~]] ~~Acts as component~~ of the ~~core factor (CF) complex which is essential for the initiation~~ of ~~rDNA transcription by~~ RNA polymerase I. ~~After binding~~ of ~~UAF (upstream activation factor)~~ to ~~an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex~~.<ref>PMID:~~8887672~~</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).	+	[[http://www.uniprot.org/uniprot/RPAC2_YEAST RPAC2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA43_YEAST RPA43_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro, the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA2_YEAST RPA2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA12_YEAST RPA12_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Involved in transcriptional termination. Involved in recruitment of RPA49 to Pol I.<ref>PMID:15073335</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 20:17, 15 November 2017

OCA — Wed, 15 Nov 2017 20:17:31 GMT

←Older revision		Revision as of 20:17, 15 November 2017
Line 11:		Line 11:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~RPAC2_YEAST RPAC2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common ~~core~~ component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/~~RPA43_YEAST RPA43_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Component~~ of RNA ~~polymerase~~ I which ~~synthesizes~~ ribosomal RNA precursors~~. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro~~, ~~the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts~~ as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, ~~CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex~~.~~<ref>PMID:8887672</ref>~~ [[http://www.uniprot.org/uniprot/~~RPA2_YEAST RPA2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Second largest core~~ component of RNA ~~polymerase~~ I which ~~synthesizes~~ ribosomal RNA precursors~~. Proposed to contribute to the polymerase catalytic activity~~ and ~~forms the polymerase active center together with the largest subunit~~. ~~Pol I is composed of mobile elements and RPA2~~ is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RPA1_YEAST RPA1_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Largest and catalytic core component~~ of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~Forms the polymerase active center together~~ with ~~the second largest subunit. A single stranded DNA template strand of the promoter~~ is ~~positioned within the central active site cleft~~ of Pol I~~. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought~~ to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters ~~and plays a role in Pol I recruitment~~. ~~After binding of UAF (upstream activation factor) to an upstream element of~~ the ~~promoter, CF is recruited in a SPT15/TBP~~-~~dependent manner to form a pre~~-~~initiation complex~~.<ref>PMID:~~21921198~~</ref> <ref>PMID:~~21940764</ref> <ref>PMID:8887672~~</ref> [[http://www.uniprot.org/uniprot/~~RPA49_YEAST RPA49_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. ~~A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired~~ transcriptional ~~activity and increased sensitivity to alpha-amanitin~~. ~~The function~~ of ~~A49 might be linked~~ to ~~the RNase H activity that was found associated with this subunit~~. [[http://www.uniprot.org/uniprot/~~RPAB2_YEAST RPAB2_YEAST~~]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~Common~~ component of RNA ~~polymerases~~ I~~, II and III~~ which ~~synthesize~~ ribosomal RNA precursors~~, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively~~. ~~Pol II is~~ the ~~central component of the basal RNA~~ polymerase ~~II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element~~ and ~~togther with parts of RPB1 and RPB2~~ forms ~~a pocket to which~~ the ~~RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA~~ polymerase ~~catalyzes~~ the ~~transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates~~. ~~Common component~~ of ~~RNA polymerases I~~ and ~~III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1~~ is part of the ~~Pol~~ core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/~~RPA12_YEAST RPA12_YEAST~~]] ~~DNA-dependent RNA polymerase catalyzes the transcription~~ of ~~DNA into RNA using~~ the ~~four ribonucleoside triphosphates as substrates. Component~~ of RNA polymerase I ~~which synthesizes ribosomal RNA precursors~~. ~~Involved in transcriptional termination. Involved in recruitment~~ of ~~RPA49~~ to ~~Pol I~~.<ref>PMID:~~15073335~~</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).	+	[[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC2_YEAST RPAC2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA43_YEAST RPA43_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro, the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA12_YEAST RPA12_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Involved in transcriptional termination. Involved in recruitment of RPA49 to Pol I.<ref>PMID:15073335</ref> [[http://www.uniprot.org/uniprot/RPA2_YEAST RPA2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:27, 8 November 2017

OCA — Wed, 08 Nov 2017 10:27:03 GMT

←Older revision		Revision as of 10:27, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='5w5y' size='340' side='right' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='5w5y' size='340' side='right' caption='[[5w5y]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/ ~~] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RRN6, YBL014C, YBL0311, YBL0312 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN7, YJL025W, J1273 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RRN11, YML043C, YM9827.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5w5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5y OCA], [http://pdbe.org/5w5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5y RCSB], [http://www.ebi.ac.uk/pdbsum/5w5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5y ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5w5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5y OCA], [http://pdbe.org/5w5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5y RCSB], [http://www.ebi.ac.uk/pdbsum/5w5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5y ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Han, Y]]		[[Category: Han, Y]]

OCA: Protected "5w5y" [edit=sysop:move=sysop]

OCA — Thu, 21 Sep 2017 04:43:21 GMT

Protected "5w5y" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:43, 21 September 2017

OCA: New page: ==RNA polymerase I Initial Transcribing Complex== == Structural h...

OCA — Thu, 21 Sep 2017 04:43:19 GMT

New page: ==RNA polymerase I Initial Transcribing Complex== <StructureSection load='5w5y' size='340' side='right' caption='5w5y, resolution 3.80Å' scene=''> == Structural h...

New page

==RNA polymerase I Initial Transcribing Complex==
<StructureSection load='5w5y' size='340' side='right' caption='[[5w5y]], [[Resolution|resolution]] 3.80Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5w5y]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_(strain_atcc_204508_/_s288c) Saccharomyces cerevisiae (strain atcc 204508 / s288c)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W5Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5w5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w5y OCA], [http://pdbe.org/5w5y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w5y RCSB], [http://www.ebi.ac.uk/pdbsum/5w5y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w5y ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/RPAC2_YEAST RPAC2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA43_YEAST RPA43_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro, the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA2_YEAST RPA2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPA12_YEAST RPA12_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Involved in transcriptional termination. Involved in recruitment of RPA49 to Pol I.<ref>PMID:15073335</ref> [[http://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 A resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.,Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y Elife. 2017 Jun 17;6. pii: e27414. doi: 10.7554/eLife.27414. PMID:28623663<ref>PMID:28623663</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w5y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: Han, Y]]
[[Category: He, Y]]
[[Category: Rna polymerase i core factor transcription]]
[[Category: Transcription]]