4r71 - Revision history

OCA at 12:50, 1 March 2024

2024-03-01T12:50:44Z

←Older revision		Revision as of 12:50, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Qbeta Escherichia virus Qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R71 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Qbeta Escherichia virus Qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R71 FirstGlance]. <br>
-	</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=4r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r71 OCA], [https://pdbe.org/4r71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r71 RCSB], [https://www.ebi.ac.uk/pdbsum/4r71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r71 ProSAT]</span></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]] 3.21Å</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=4r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r71 OCA], [https://pdbe.org/4r71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r71 RCSB], [https://www.ebi.ac.uk/pdbsum/4r71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r71 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/EFTU2_ECOLI EFTU2_ECOLI] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118][https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050]		[https://www.uniprot.org/uniprot/EFTU2_ECOLI EFTU2_ECOLI] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118][https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Upon infection of Escherichia coli by bacteriophage Qbeta, the virus-encoded beta-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qbeta replicase holoenzyme complex, which is responsible for amplifying the Qbeta (+)-RNA genome. Here, we use X-ray crystallography, NMR spectroscopy, as well as sequence conservation, surface electrostatic potential and mutational analyses to decipher the roles of the beta-subunit and the first two oligonucleotide-oligosaccharide-binding domains of S1 (OB1-2) in the recognition of Qbeta (+)-RNA by the Qbeta replicase complex. We show how three basic residues of the beta subunit form a patch located adjacent to the OB2 domain, and use NMR spectroscopy to demonstrate for the first time that OB2 is able to interact with RNA. Neutralization of the basic residues by mutagenesis results in a loss of both the phage infectivity in vivo and the ability of Qbeta replicase to amplify the genomic RNA in vitro. In contrast, replication of smaller replicable RNAs is not affected. Taken together, our data suggest that the beta-subunit and protein S1 cooperatively bind the (+)-stranded Qbeta genome during replication initiation and provide a foundation for understanding template discrimination during replication initiation.
-
-	Structural basis for RNA-genome recognition during bacteriophage Qbeta replication.,Gytz H, Mohr D, Seweryn P, Yoshimura Y, Kutlubaeva Z, Dolman F, Chelchessa B, Chetverin AB, Mulder FA, Brodersen DE, Knudsen CR Nucleic Acids Res. 2015 Dec 15;43(22):10893-906. doi: 10.1093/nar/gkv1212. Epub, 2015 Nov 17. PMID:26578560<ref>PMID:26578560</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 14:
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	*[[Ribosomal protein S1\|Ribosomal protein S1]]		*[[Ribosomal protein S1\|Ribosomal protein S1]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:42, 2 March 2023

2023-03-02T06:42:39Z

←Older revision		Revision as of 06:42, 2 March 2023
Line 3:		Line 3:
	<StructureSection load='4r71' size='340' side='right'caption='[[4r71]], [[Resolution\|resolution]] 3.21Å' scene=''>		<StructureSection load='4r71' size='340' side='right'caption='[[4r71]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4R71 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Qbeta Escherichia virus Qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R71 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>	+	</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=4r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r71 OCA], [https://pdbe.org/4r71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r71 RCSB], [https://www.ebi.ac.uk/pdbsum/4r71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r71 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=4r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r71 OCA], [~~http~~://pdbe.org/4r71 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4r71 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4r71 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4r71 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[http://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[http://www.uniprot.org/uniprot/RDRP_BPQBE RDRP_BPQBE]] This enzyme is part of the viral RNA-dependent RNA polymerase complex.	+	[https://www.uniprot.org/uniprot/EFTU2_ECOLI EFTU2_ECOLI] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118][https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
		+	[[Category: Escherichia virus Qbeta]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: RNA-directed RNA polymerase]]~~	+	[[Category: Brodersen DE]]
-	[[Category: Brodersen~~, D E~~]]	+	[[Category: Chetverin AB]]
-	[[Category: Chetverin~~, A B~~]]	+	[[Category: Gytz H]]
-	[[Category: Gytz, H]]	+	[[Category: Knudsen CR]]
-	[[Category: Knudsen~~, C R~~]]	+	[[Category: Kutlubaeva Z]]
-	[[Category: Kutlubaeva, Z]]	+	[[Category: Seweryn P]]
-	[[Category: Seweryn, P]]	+
-	~~[[Category: Ob fold]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Viral protein-ribosomal protein complex~~]]	+

OCA at 07:55, 19 February 2020

2020-02-19T07:55:43Z

←Older revision		Revision as of 07:55, 19 February 2020
Line 1:		Line 1:

	==Structure of the Qbeta holoenzyme complex in the P1211 crystal form==		==Structure of the Qbeta holoenzyme complex in the P1211 crystal form==
-	<StructureSection load='4r71' size='340' side='right' caption='[[4r71]], [[Resolution\|resolution]] 3.21Å' scene=''>	+	<StructureSection load='4r71' size='340' side='right'caption='[[4r71]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R71 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R71 FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Ribosomal protein S1\|Ribosomal protein S1]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: RNA-directed RNA polymerase]]		[[Category: RNA-directed RNA polymerase]]
	[[Category: Brodersen, D E]]		[[Category: Brodersen, D E]]

OCA at 11:13, 16 November 2017

2017-11-16T11:13:20Z

←Older revision		Revision as of 11:13, 16 November 2017
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Elongation factor\|Elongation factor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:14, 3 August 2017

2017-08-03T08:14:08Z

←Older revision		Revision as of 08:14, 3 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4r71 is ~~ON HOLD~~	+	==Structure of the Qbeta holoenzyme complex in the P1211 crystal form==
		+	<StructureSection load='4r71' size='340' side='right' caption='[[4r71]], [[Resolution\|resolution]] 3.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4r71]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R71 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R71 FirstGlance]. <br>
		+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=4r71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r71 OCA], [http://pdbe.org/4r71 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4r71 RCSB], [http://www.ebi.ac.uk/pdbsum/4r71 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4r71 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[http://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[http://www.uniprot.org/uniprot/RDRP_BPQBE RDRP_BPQBE]] This enzyme is part of the viral RNA-dependent RNA polymerase complex.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Upon infection of Escherichia coli by bacteriophage Qbeta, the virus-encoded beta-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qbeta replicase holoenzyme complex, which is responsible for amplifying the Qbeta (+)-RNA genome. Here, we use X-ray crystallography, NMR spectroscopy, as well as sequence conservation, surface electrostatic potential and mutational analyses to decipher the roles of the beta-subunit and the first two oligonucleotide-oligosaccharide-binding domains of S1 (OB1-2) in the recognition of Qbeta (+)-RNA by the Qbeta replicase complex. We show how three basic residues of the beta subunit form a patch located adjacent to the OB2 domain, and use NMR spectroscopy to demonstrate for the first time that OB2 is able to interact with RNA. Neutralization of the basic residues by mutagenesis results in a loss of both the phage infectivity in vivo and the ability of Qbeta replicase to amplify the genomic RNA in vitro. In contrast, replication of smaller replicable RNAs is not affected. Taken together, our data suggest that the beta-subunit and protein S1 cooperatively bind the (+)-stranded Qbeta genome during replication initiation and provide a foundation for understanding template discrimination during replication initiation.

-	~~Authors: Olesen~~, H~~.G.~~, ~~Seweryn~~, P., Brodersen, D.E.~~, Knudsen, C~~.R.	+	Structural basis for RNA-genome recognition during bacteriophage Qbeta replication.,Gytz H, Mohr D, Seweryn P, Yoshimura Y, Kutlubaeva Z, Dolman F, Chelchessa B, Chetverin AB, Mulder FA, Brodersen DE, Knudsen CR Nucleic Acids Res. 2015 Dec 15;43(22):10893-906. doi: 10.1093/nar/gkv1212. Epub, 2015 Nov 17. PMID:26578560<ref>PMID:26578560</ref>

-	~~Description: Structure~~ of the ~~Qbeta holoenzyme complex in the P1211 crystal form~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Brodersen, D.E]]	+	<div class="pdbe-citations 4r71" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Olesen~~, H.G]]	+
-	[[Category: Knudsen, C.R]]	+	==See Also==
		+	*[[Elongation factor\|Elongation factor]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: RNA-directed RNA polymerase]]
		+	[[Category: Brodersen, D E]]
		+	[[Category: Chetverin, A B]]
		+	[[Category: Gytz, H]]
		+	[[Category: Knudsen, C R]]
		+	[[Category: Kutlubaeva, Z]]
	[[Category: Seweryn, P]]		[[Category: Seweryn, P]]
		+	[[Category: Ob fold]]
		+	[[Category: Translation]]
		+	[[Category: Viral protein-ribosomal protein complex]]

OCA at 05:46, 9 September 2015

2015-09-09T05:46:52Z

←Older revision		Revision as of 05:46, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4r71 is ON HOLD ~~until Sep 26 2016~~	+	The entry 4r71 is ON HOLD

	Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.		Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.

OCA at 14:38, 5 August 2015

2015-08-05T14:38:06Z

←Older revision		Revision as of 14:38, 5 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4r71 is ON HOLD until ~~Paper Publication~~	+	The entry 4r71 is ON HOLD until Sep 26 2016

	Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.		Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.

OCA at 16:34, 24 December 2014

2014-12-24T16:34:15Z

←Older revision		Revision as of 16:34, 24 December 2014
Line 6:		Line 6:

	Description: Structure of the Qbeta holoenzyme complex in the P1211 crystal form		Description: Structure of the Qbeta holoenzyme complex in the P1211 crystal form
		+	[[Category: Unreleased Structures]]
		+	[[Category: Brodersen, D.E]]
		+	[[Category: Olesen, H.G]]
		+	[[Category: Knudsen, C.R]]
		+	[[Category: Seweryn, P]]

OCA at 10:03, 29 October 2014

2014-10-29T10:03:08Z

←Older revision		Revision as of 10:03, 29 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4r71 is ON HOLD	+	The entry 4r71 is ON HOLD until Paper Publication

	Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.		Authors: Olesen, H.G., Seweryn, P., Brodersen, D.E., Knudsen, C.R.

	Description: Structure of the Qbeta holoenzyme complex in the P1211 crystal form		Description: Structure of the Qbeta holoenzyme complex in the P1211 crystal form

OCA: Protected "4r71" [edit=sysop:move=sysop]

2014-09-04T04:18:07Z

Protected "4r71" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:18, 4 September 2014