5dma - Revision history

OCA at 21:49, 28 June 2023

2023-06-28T21:49:27Z

←Older revision		Revision as of 21:49, 28 June 2023
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	<StructureSection load='5dma' size='340' side='right'caption='[[5dma]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='5dma' size='340' side='right'caption='[[5dma]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dma]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_12980 Atcc 12980~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DMA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DMA FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pcrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=1422 ATCC 12980])</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]] 1.53Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/DNA_helicase DNA helicase~~]~~, with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=5dma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dma OCA], [https://pdbe.org/5dma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dma RCSB], [https://www.ebi.ac.uk/pdbsum/5dma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dma 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=5dma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dma OCA], [~~http~~://pdbe.org/5dma PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dma RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dma PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dma ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCRA_GEOSE PCRA_GEOSE]] DNA helicase. Has a broad nucleotide specificity, even being able to hydrolyze ethenonucleotides, and is able to couple the hydrolysis to unwinding of DNA substrates. It is a 3'-5' helicase but at high protein concentrations it can also displace a substrate with a 5' tail. Preferred substrate being one with both single and double-stranded regions of DNA.	+	[https://www.uniprot.org/uniprot/PCRA_GEOSE PCRA_GEOSE] DNA helicase. Has a broad nucleotide specificity, even being able to hydrolyze ethenonucleotides, and is able to couple the hydrolysis to unwinding of DNA substrates. It is a 3'-5' helicase but at high protein concentrations it can also displace a substrate with a 5' tail. Preferred substrate being one with both single and double-stranded regions of DNA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 12980]]~~	+	[[Category: Geobacillus stearothermophilus]]
-	~~[[Category: DNA helicase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dillingham, M]]	+	[[Category: Dillingham M]]
-	[[Category: Lin~~, C L~~]]	+	[[Category: Lin CL]]
-	[[Category: Wigley, D]]	+	[[Category: Wigley D]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pcra/uvrd helicase]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Tudor domain~~]]	+

OCA at 08:09, 8 April 2020

2020-04-08T08:09:55Z

←Older revision		Revision as of 08:09, 8 April 2020
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	==Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase==		==Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase==
-	<StructureSection load='5dma' size='340' side='right' caption='[[5dma]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='5dma' size='340' side='right'caption='[[5dma]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DMA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dma]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DMA 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/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcrA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 ATCC 12980])</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=5dma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dma OCA], [http://pdbe.org/5dma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dma RCSB], [http://www.ebi.ac.uk/pdbsum/5dma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dma ProSAT]</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_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=5dma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dma OCA], [http://pdbe.org/5dma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dma RCSB], [http://www.ebi.ac.uk/pdbsum/5dma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dma ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5dma" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5dma" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Helicase 3D structures\|Helicase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 12980]]
	[[Category: DNA helicase]]		[[Category: DNA helicase]]
		+	[[Category: Large Structures]]
	[[Category: Dillingham, M]]		[[Category: Dillingham, M]]
	[[Category: Lin, C L]]		[[Category: Lin, C L]]

OCA at 06:18, 4 May 2017

2017-05-04T06:18:03Z

←Older revision		Revision as of 06:18, 4 May 2017
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PCRA_GEOSE PCRA_GEOSE]] DNA helicase. Has a broad nucleotide specificity, even being able to hydrolyze ethenonucleotides, and is able to couple the hydrolysis to unwinding of DNA substrates. It is a 3'-5' helicase but at high protein concentrations it can also displace a substrate with a 5' tail. Preferred substrate being one with both single and double-stranded regions of DNA.		[[http://www.uniprot.org/uniprot/PCRA_GEOSE PCRA_GEOSE]] DNA helicase. Has a broad nucleotide specificity, even being able to hydrolyze ethenonucleotides, and is able to couple the hydrolysis to unwinding of DNA substrates. It is a 3'-5' helicase but at high protein concentrations it can also displace a substrate with a 5' tail. Preferred substrate being one with both single and double-stranded regions of DNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The PcrA/UvrD helicase functions in multiple pathways that promote bacterial genome stability including the suppression of conflicts between replication and transcription and facilitating the repair of transcribed DNA. The reported ability of PcrA/UvrD to bind and backtrack RNA polymerase (1,2) might be relevant to these functions, but the structural basis for this activity is poorly understood. In this work, we define a minimal RNA polymerase interaction domain in PcrA, and report its crystal structure at 1.5 A resolution. The domain adopts a Tudor-like fold that is similar to other RNA polymerase interaction domains, including that of the prototype transcription-repair coupling factor Mfd. Removal or mutation of the interaction domain reduces the ability of PcrA/UvrD to interact with and to remodel RNA polymerase complexes in vitro. The implications of this work for our understanding of the role of PcrA/UvrD at the interface of DNA replication, transcription and repair are discussed.
		+
		+	The structure and function of an RNA polymerase interaction domain in the PcrA/UvrD helicase.,Sanders K, Lin CL, Smith AJ, Cronin N, Fisher G, Eftychidis V, McGlynn P, Savery NJ, Wigley DB, Dillingham MS Nucleic Acids Res. 2017 Apr 20;45(7):3875-3887. doi: 10.1093/nar/gkx074. PMID:28160601<ref>PMID:28160601</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5dma" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:03, 3 October 2016

2016-10-03T17:03:32Z

←Older revision		Revision as of 17:03, 3 October 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5dma is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase==
-		+	<StructureSection load='5dma' size='340' side='right' caption='[[5dma]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~Authors~~: ~~Lin~~, C.L., ~~Dillingham~~, M., ~~Wigley~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5dma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DMA FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of C-~~terminal tudor domain in PcrA/UvrD~~ helicase	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5dma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dma OCA], [http://pdbe.org/5dma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dma RCSB], [http://www.ebi.ac.uk/pdbsum/5dma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dma ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCRA_GEOSE PCRA_GEOSE]] DNA helicase. Has a broad nucleotide specificity, even being able to hydrolyze ethenonucleotides, and is able to couple the hydrolysis to unwinding of DNA substrates. It is a 3'-5' helicase but at high protein concentrations it can also displace a substrate with a 5' tail. Preferred substrate being one with both single and double-stranded regions of DNA.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA helicase]]
	[[Category: Dillingham, M]]		[[Category: Dillingham, M]]
		+	[[Category: Lin, C L]]
	[[Category: Wigley, D]]		[[Category: Wigley, D]]
-	[[Category: ~~Lin, C.L~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Pcra/uvrd helicase]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Transcription]]
		+	[[Category: Tudor domain]]

OCA at 09:15, 27 July 2016

2016-07-27T09:15:16Z

←Older revision		Revision as of 09:15, 27 July 2016
Line 3:		Line 3:
	The entry 5dma is ON HOLD until Paper Publication		The entry 5dma is ON HOLD until Paper Publication

-	Authors: ~~Wigley~~, D., Dillingham, M., ~~Lin~~, ~~C.L~~.	+	Authors: Lin, C.L., Dillingham, M., Wigley, D.

	Description: Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase		Description: Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase

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

2015-09-30T13:09:40Z

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

←Older revision

Revision as of 13:09, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5dma is ON HOLD until Paper Publication Authors: Wigley, D., Dillingham, M., Lin, C.L. Description: Crystal structure of C-terminal tudor domain in...

2015-09-30T13:09:39Z

New page: '''Unreleased structure''' The entry 5dma is ON HOLD until Paper Publication Authors: Wigley, D., Dillingham, M., Lin, C.L. Description: Crystal structure of C-terminal tudor domain in...

New page

'''Unreleased structure'''

The entry 5dma is ON HOLD until Paper Publication

Authors: Wigley, D., Dillingham, M., Lin, C.L.

Description: Crystal structure of C-terminal tudor domain in PcrA/UvrD helicase
[[Category: Unreleased Structures]]
[[Category: Dillingham, M]]
[[Category: Wigley, D]]
[[Category: Lin, C.L]]