6lw3 - Revision history

OCA at 14:58, 29 November 2023

2023-11-29T14:58:52Z

←Older revision		Revision as of 14:58, 29 November 2023
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	<StructureSection load='6lw3' size='340' side='right'caption='[[6lw3]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='6lw3' size='340' side='right'caption='[[6lw3]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LW3 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">ruvC, C0044_06995, CAZ10_11430, CGU42_02205, CKA47_33020, DY930_19340, DZ934_18445, DZ962_02435, E4V10_33000, EQH76_21345, FCG96_31605, FLI88_33360, IPC1481_05880, IPC1482_18775, IPC165_11875, IPC170_03130, IPC47_08385, IPC669_29490, RW109_RW109_05217 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~287~~ "~~Bacillus aeruginosus~~" ~~(Schroeter 1872) Trevisan 1885])</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]] 2.38Å</td></tr>
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'~~>[~~https://en.wikipedia.org/wiki/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease~~]~~, with EC number [https://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </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=6lw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lw3 OCA], [https://pdbe.org/6lw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lw3 RCSB], [https://www.ebi.ac.uk/pdbsum/6lw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lw3 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=6lw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lw3 OCA], [https://pdbe.org/6lw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lw3 RCSB], [https://www.ebi.ac.uk/pdbsum/6lw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lw3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~A0A0C7D4E1_PSEAI A0A0C7D4E1_PSEAI~~]~~] Nuclease that resolves~~ Holliday junction ~~intermediates in~~ genetic recombination. Cleaves ~~the~~ cruciform ~~structure in supercoiled~~ DNA by ~~nicking to strands with~~ the ~~same polarity~~ at ~~sites symmetrically opposed at the junction in~~ the homologous arms ~~and leaves~~ a 5'-~~terminal~~ phosphate and a 3'-~~terminal~~ hydroxyl group.[HAMAP-Rule:MF_00034]~~[SAAS~~:~~SAAS01093222]~~	+	[https://www.uniprot.org/uniprot/RUVC_PSEAE RUVC_PSEAE] The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair. Endonuclease that resolves HJ intermediates. Cleaves cruciform DNA by making single-stranded nicks across the HJ at symmetrical positions within the homologous arms, yielding a 5'-phosphate and a 3'-hydroxyl group; requires a central core of homology in the junction. The consensus cleavage sequence is 5'-(A/T)TT(C/G)-3'. Cleavage occurs on the 3'-side of the TT dinucleotide at the point of strand exchange. HJ branch migration catalyzed by RuvA-RuvB allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves the cruciform DNA.[HAMAP-Rule:MF_00034] Complements an E.coli deletion mutant (PubMed:8982068). A C-terminally truncated protein (residues 1-153) binds cruciform but not linear dsDNA, the consensus cleavage sequence is 5'-TT\|C-3' (PubMed:32085896).<ref>PMID:32085896</ref> <ref>PMID:8982068</ref>
	<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: Crossover junction endodeoxyribonuclease]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~He, Y~~]]	+	[[Category: Pseudomonas aeruginosa]]
-	[[Category: ~~Hu,~~ Y]]	+	[[Category: He Y]]
-	[[Category: ~~Lin, Z~~]]	+	[[Category: Hu Y]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Lin Z]]
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Holliday junction]]~~	+
-	~~[[Category: Resolvase]]~~	+
-	~~[[Category: Ruvc~~]]	+

OCA at 10:44, 16 February 2022

2022-02-16T10:44:32Z

←Older revision		Revision as of 10:44, 16 February 2022
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	<StructureSection load='6lw3' size='340' side='right'caption='[[6lw3]], [[Resolution\|resolution]] 2.38Å' scene=''>		<StructureSection load='6lw3' size='340' side='right'caption='[[6lw3]], [[Resolution\|resolution]] 2.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6lw3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LW3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6LW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6lw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LW3 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/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ruvC, C0044_06995, CAZ10_11430, CGU42_02205, CKA47_33020, DY930_19340, DZ934_18445, DZ962_02435, E4V10_33000, EQH76_21345, FCG96_31605, FLI88_33360, IPC1481_05880, IPC1482_18775, IPC165_11875, IPC170_03130, IPC47_08385, IPC669_29490, RW109_RW109_05217 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 "Bacillus aeruginosus" (Schroeter 1872) Trevisan 1885])</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=6lw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lw3 OCA], [~~http~~://pdbe.org/6lw3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6lw3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6lw3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6lw3 ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </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=6lw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lw3 OCA], [https://pdbe.org/6lw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lw3 RCSB], [https://www.ebi.ac.uk/pdbsum/6lw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lw3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/A0A0C7D4E1_PSEAI A0A0C7D4E1_PSEAI]] Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group.[HAMAP-Rule:MF_00034][SAAS:SAAS01093222]	+	[[https://www.uniprot.org/uniprot/A0A0C7D4E1_PSEAI A0A0C7D4E1_PSEAI]] Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group.[HAMAP-Rule:MF_00034][SAAS:SAAS01093222]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Holliday junction, a four-way DNA structure, is an important intermediate of homologous recombination. Proper Holliday junction resolution is critical to complete the recombination process. In most bacterial cells, the Holliday junction cleavage is mainly performed by a specific endonuclease RuvC. Here, we describe the biochemical properties and the crystal structure of RuvC from an opportunistic pathogen, Pseudomonas aeruginosa (PaRuvC). PaRuvC specifically binds to the Holliday junction DNA and preferentially cleaves it at the consensus 5'-TTC-3'. PaRuvC uses Mg(2+) as the preferred divalent metal cofactor for Holliday junction cleavage and its optimum pH is 8.0-9.0. Elevated temperatures (37-60 degrees C) boost the catalytic activity, but temperatures higher than 53 degrees C reduce the protein stability. The crystal structure of PaRuvC determined at 2.4 A and mutagenesis analysis reveal key residues involved in the dimer formation, substrate binding and catalysis. Our results are expected to provide useful information to combat antibiotic resistance of Pseudomonas aeruginosa by targeting its homologous recombination system.
		+
		+	Biochemical and structural characterization of the Holliday junction resolvase RuvC from Pseudomonas aeruginosa.,Hu Y, He Y, Lin Z Biochem Biophys Res Commun. 2020 Apr 30;525(2):265-271. doi:, 10.1016/j.bbrc.2020.02.062. Epub 2020 Feb 19. PMID:32085896<ref>PMID:32085896</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6lw3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Resolvase 3D structures\|Resolvase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:16, 26 February 2020

2020-02-26T09:16:01Z

←Older revision		Revision as of 09:16, 26 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6lw3 is ~~ON HOLD~~	+	==Crystal structure of RuvC from Pseudomonas aeruginosa==
-		+	<StructureSection load='6lw3' size='340' side='right'caption='[[6lw3]], [[Resolution\|resolution]] 2.38Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6lw3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LW3 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Crossover_junction_endodeoxyribonuclease Crossover junction endodeoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.22.4 3.1.22.4] </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=6lw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lw3 OCA], [http://pdbe.org/6lw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6lw3 RCSB], [http://www.ebi.ac.uk/pdbsum/6lw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6lw3 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0C7D4E1_PSEAI A0A0C7D4E1_PSEAI]] Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group.[HAMAP-Rule:MF_00034][SAAS:SAAS01093222]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Crossover junction endodeoxyribonuclease]]
		+	[[Category: Large Structures]]
		+	[[Category: He, Y]]
		+	[[Category: Hu, Y]]
		+	[[Category: Lin, Z]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Endonuclease]]
		+	[[Category: Holliday junction]]
		+	[[Category: Resolvase]]
		+	[[Category: Ruvc]]

OCA: Protected "6lw3" [edit=sysop:move=sysop]

2020-02-13T02:35:26Z

Protected "6lw3" [edit=sysop:move=sysop]

←Older revision

Revision as of 02:35, 13 February 2020

OCA: New page: '''Unreleased structure''' The entry 6lw3 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-02-13T02:35:24Z

New page: '''Unreleased structure''' The entry 6lw3 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6lw3 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]