2b3t - Revision history

OCA at 09:15, 14 February 2024

2024-02-14T09:15:51Z

←Older revision		Revision as of 09:15, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='2b3t' size='340' side='right'caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='2b3t' size='340' side='right'caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B3T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>hemK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895]), prfA, sueB, uar ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])~~</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [https://pdbe.org/2b3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [https://www.ebi.ac.uk/pdbsum/2b3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3t ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [https://pdbe.org/2b3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [https://www.ebi.ac.uk/pdbsum/2b3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PRMC_ECOLI PRMC_ECOLI]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[https://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]	+	[https://www.uniprot.org/uniprot/PRMC_ECOLI PRMC_ECOLI] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2b3t ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2b3t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center. The glutamine side chain of this motif is specifically methylated in both prokaryotes and eukaryotes. Methylation in E. coli is due to PrmC and results in strong stimulation of peptide chain release. We have solved the crystal structure of the complex between E. coli RF1 and PrmC bound to the methyl donor product AdoHCy. Both the GGQ domain (domain 3) and the central region (domains 2 and 4) of RF1 interact with PrmC. Structural and mutagenic data indicate a compact conformation of RF1 that is unlike its conformation when it is bound to the ribosome but is similar to the crystal structure of the protein alone.
-
-	Molecular basis for bacterial class I release factor methylation by PrmC.,Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH Mol Cell. 2005 Dec 22;20(6):917-27. PMID:16364916<ref>PMID:16364916</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2b3t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Buckingham~~, R H~~]]	+	[[Category: Buckingham RH]]
-	[[Category: Champ, S]]	+	[[Category: Champ S]]
-	[[Category: Graille, M]]	+	[[Category: Graille M]]
-	[[Category: Heurgue-Hamard, V]]	+	[[Category: Heurgue-Hamard V]]
-	[[Category: Mora, L]]	+	[[Category: Mora L]]
-	[[Category: Scrima, N]]	+	[[Category: Scrima N]]
-	~~[[Category: Tilbeurgh, H van~~]]	+	[[Category: Ulryck N]]
-	[[Category: Ulryck, N]]	+	[[Category: Van Tilbeurgh H]]
-	[[Category: ~~Conformational change]]~~	+
-	~~[[Category: Methylation]]~~	+
-	~~[[Category: Release factor]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Translation termination~~]]	+

OCA at 11:33, 3 February 2021

2021-02-03T11:33:48Z

←Older revision		Revision as of 11:33, 3 February 2021
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	==Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase==		==Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase==
-	<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='2b3t' size='340' side='right'caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2B3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B3T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfA, sueB, uar ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfA, sueB, uar ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [~~http~~://pdbe.org/2b3t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2b3t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3t ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [https://pdbe.org/2b3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [https://www.ebi.ac.uk/pdbsum/2b3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PRMC_ECOLI PRMC_ECOLI]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[~~http~~://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]	+	[[https://www.uniprot.org/uniprot/PRMC_ECOLI PRMC_ECOLI]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[https://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Buckingham, R H]]		[[Category: Buckingham, R H]]
	[[Category: Champ, S]]		[[Category: Champ, S]]

OCA at 06:45, 15 February 2018

2018-02-15T06:45:28Z

←Older revision		Revision as of 06:45, 15 February 2018
Line 1:		Line 1:

-	==~~Molecular basis for bacterial class 1 release~~ factor ~~methylation by~~ PrmC==	+	==Structure of complex between E. coli translation termination factor RF1 and the PrmC methyltransferase==
	<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/2b3t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/2b3t_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:35, 12 October 2017

2017-10-12T09:35:38Z

←Older revision		Revision as of 09:35, 12 October 2017
Line 1:		Line 1:
		+
	==Molecular basis for bacterial class 1 release factor methylation by PrmC==		==Molecular basis for bacterial class 1 release factor methylation by PrmC==
	<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://pdbe.org/2b3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://pdbe.org/2b3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2b3t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:04, 11 September 2015

2015-09-11T17:04:01Z

←Older revision		Revision as of 17:04, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B3T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B3T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://pdbe.org/2b3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~HEMK_ECOLI HEMK_ECOLI~~]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[http://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]	+	[[http://www.uniprot.org/uniprot/PRMC_ECOLI PRMC_ECOLI]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[http://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2b3t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Buckingham, R H]]		[[Category: Buckingham, R H]]
	[[Category: Champ, S]]		[[Category: Champ, S]]

OCA at 19:22, 25 December 2014

2014-12-25T19:22:12Z

←Older revision		Revision as of 19:22, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B3T FirstGlance]. <br>		<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B3T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</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=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HEMK_ECOLI HEMK_ECOLI]] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif, i.e. on 'Gln-235' in RF1 and on 'Gln-252' in RF2.<ref>PMID:11805295</ref> <ref>PMID:11847124</ref> <ref>PMID:16364916</ref> [[http://www.uniprot.org/uniprot/RF1_ECOLI RF1_ECOLI]] Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA.[HAMAP-Rule:MF_00093]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Buckingham, R H.]]	+	[[Category: Buckingham, R H]]
-	[[Category: Champ, S.]]	+	[[Category: Champ, S]]
-	[[Category: Graille, M.]]	+	[[Category: Graille, M]]
-	[[Category: Heurgue-Hamard, V.]]	+	[[Category: Heurgue-Hamard, V]]
-	[[Category: Mora, L.]]	+	[[Category: Mora, L]]
-	[[Category: Scrima, N.]]	+	[[Category: Scrima, N]]
-	[[Category: Tilbeurgh, H van.]]	+	[[Category: Tilbeurgh, H van]]
-	[[Category: Ulryck, N.]]	+	[[Category: Ulryck, N]]
	[[Category: Conformational change]]		[[Category: Conformational change]]
	[[Category: Methylation]]		[[Category: Methylation]]

OCA at 00:26, 30 September 2014

2014-09-30T00:26:15Z

←Older revision		Revision as of 00:26, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2b3t.~~png~~\|~~left~~\|200px]]	+	==Molecular basis for bacterial class 1 release factor methylation by PrmC==
		+	<StructureSection load='2b3t' size='340' side='right' caption='[[2b3t]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B3T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ml5\|1ml5]], [[1gqe\|1gqe]], [[1nv8\|1nv8]], [[1t43\|1t43]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hemK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), prfA, sueB, uar ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b3t RCSB], [http://www.ebi.ac.uk/pdbsum/2b3t PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b3/2b3t_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Class I release factors bind to ribosomes in response to stop codons and trigger peptidyl-tRNA hydrolysis at the P site. Prokaryotic and eukaryotic RFs share one motif: a GGQ tripeptide positioned in a loop at the end of a stem region that interacts with the ribosomal peptidyl transferase center. The glutamine side chain of this motif is specifically methylated in both prokaryotes and eukaryotes. Methylation in E. coli is due to PrmC and results in strong stimulation of peptide chain release. We have solved the crystal structure of the complex between E. coli RF1 and PrmC bound to the methyl donor product AdoHCy. Both the GGQ domain (domain 3) and the central region (domains 2 and 4) of RF1 interact with PrmC. Structural and mutagenic data indicate a compact conformation of RF1 that is unlike its conformation when it is bound to the ribosome but is similar to the crystal structure of the protein alone.

-	~~{{STRUCTURE_2b3t\| PDB=2b3t \| SCENE= }}~~	+	Molecular basis for bacterial class I release factor methylation by PrmC.,Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH Mol Cell. 2005 Dec 22;20(6):917-27. PMID:16364916<ref>PMID:16364916</ref>

-	~~===Molecular basis for bacterial class 1 release factor methylation by PrmC===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16364916}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2b3t]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016364916<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Buckingham, R H.]]		[[Category: Buckingham, R H.]]

OCA: Protected "2b3t" [edit=sysop:move=sysop]

2013-01-06T09:49:16Z

Protected "2b3t" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:49, 6 January 2013

OCA at 09:49, 6 January 2013

2013-01-06T09:49:13Z

←Older revision		Revision as of 09:49, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2b3t.png\|left\|200px]]		[[Image:2b3t.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2b3t", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2b3t\| PDB=2b3t \| SCENE= }}		{{STRUCTURE_2b3t\| PDB=2b3t \| SCENE= }}

	===Molecular basis for bacterial class 1 release factor methylation by PrmC===		===Molecular basis for bacterial class 1 release factor methylation by PrmC===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16364916}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16364916 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_16364916}}		{{ABSTRACT_PUBMED_16364916}}

	==About this Structure==		==About this Structure==
-	~~2B3T~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA].	+	[[2b3t]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16364916~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016364916</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Buckingham, R H.]]		[[Category: Buckingham, R H.]]
Line 36:		Line 24:
	[[Category: Methylation]]		[[Category: Methylation]]
	[[Category: Release factor]]		[[Category: Release factor]]
		+	[[Category: Translation]]
	[[Category: Translation termination]]		[[Category: Translation termination]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:21:38 2009''

OCA at 02:21, 18 February 2009

2009-02-18T02:21:40Z

←Older revision		Revision as of 02:21, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2B3T is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA].	+	2B3T is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3T OCA].

	==Reference==		==Reference==
-	Molecular basis for bacterial class I release factor methylation by PrmC., Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH, Mol Cell. 2005 Dec 22;20(6):917-27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16364916 16364916]~~	+	<ref group="xtra">PMID:16364916</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Protein complex]]
	[[Category: Buckingham, R H.]]		[[Category: Buckingham, R H.]]
	[[Category: Champ, S.]]		[[Category: Champ, S.]]
Line 39:		Line 38:
	[[Category: Translation termination]]		[[Category: Translation termination]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 11~~:00:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:21:38 2009''