4xpu - Revision history

OCA at 15:30, 8 November 2023

OCA — Wed, 08 Nov 2023 15:30:28 GMT

←Older revision		Revision as of 15:30, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPU 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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [https://pdbe.org/4xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [https://www.ebi.ac.uk/pdbsum/4xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpu 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]] 2.4Å</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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [https://pdbe.org/4xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [https://www.ebi.ac.uk/pdbsum/4xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 17:47, 26 April 2023

OCA — Wed, 26 Apr 2023 17:47:00 GMT

←Older revision		Revision as of 17:47, 26 April 2023
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	<StructureSection load='4xpu' size='340' side='right'caption='[[4xpu]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4xpu' size='340' side='right'caption='[[4xpu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco45 Eco45~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XPU FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi, ECS88_4459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45])</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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [https://pdbe.org/4xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [https://www.ebi.ac.uk/pdbsum/4xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpu 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/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [~~http~~://pdbe.org/4xpu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xpu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NFI_ECO45 NFI_ECO45]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA.	+	[https://www.uniprot.org/uniprot/NFI_ECO45 NFI_ECO45] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deoxyribonuclease V]]~~	+	[[Category: Escherichia coli S88]]
-	~~[[Category: Eco45~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Xie, W]]	+	[[Category: Xie W]]
-	[[Category: Zhang, Z]]	+	[[Category: Zhang Z]]
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Endonuclease v]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inosine]]~~	+
-	~~[[Category: Rna cleavage~~]]	+

OCA at 23:39, 5 June 2019

OCA — Wed, 05 Jun 2019 23:39:52 GMT

←Older revision		Revision as of 23:39, 5 June 2019
Line 1:		Line 1:
		+
	==The crystal structure of EndoV from E.coli==		==The crystal structure of EndoV from E.coli==
-	<StructureSection load='4xpu' size='340' side='right' caption='[[4xpu]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4xpu' size='340' side='right'caption='[[4xpu]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco45 Eco45]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPU 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/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nfi, ECS88_4459 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45])</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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [http://www.ebi.ac.uk/pdbsum/4xpu PDBsum]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [http://pdbe.org/4xpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [http://www.ebi.ac.uk/pdbsum/4xpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xpu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4xpu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Deoxyribonuclease V]]		[[Category: Deoxyribonuclease V]]
		+	[[Category: Eco45]]
		+	[[Category: Large Structures]]
	[[Category: Xie, W]]		[[Category: Xie, W]]
	[[Category: Zhang, Z]]		[[Category: Zhang, Z]]

OCA at 12:12, 20 August 2015

OCA — Thu, 20 Aug 2015 12:12:56 GMT

←Older revision		Revision as of 12:12, 20 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==The crystal structure of EndoV from E.coli==
		+	<StructureSection load='4xpu' size='340' side='right' caption='[[4xpu]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xpu]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XPU 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/Deoxyribonuclease_V Deoxyribonuclease V], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.7 3.1.21.7] </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=4xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xpu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xpu RCSB], [http://www.ebi.ac.uk/pdbsum/4xpu PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NFI_ECO45 NFI_ECO45]] DNA repair enzyme involved in the repair of deaminated bases. Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Endonuclease V (EndoV) is a ubiquitous protein present in all three kingdoms of life, responsible for the specific cleavages at the second phosphodiester bond 3' to inosine. E. coli EndoV (EcEndoV) is the first member discovered in the EndoV family. It is a small protein with a compact gene organization, yet with a wide spectrum of substrate specificities. However, the structural basis of its substrate recognition is not well understood. In this study, we determined the 2.4 A crystal structure of EcEndoV. The enzyme preserves the general 'RNase H-like motif' structure. Two subunits are almost fully resolved in the asymmetric unit, but they are not related by any 2-fold axes. Rather, they establish "head-to-shoulder" contacts with loose interactions between each other. Mutational studies show that mutations that disrupt the association mode of the two subunits also decrease the cleavage efficiencies of the enzyme. Further biochemical studies suggest that EcEndoV is able to bind to single-stranded, undamaged DNA substrates without sequence specificity, and forms two types of complexes in a metal-independent manner, which may explain the wide spectrum of substrate specificities of EcEndoV.

-	~~The entry 4xpu is ON HOLD until Jan 18 2017~~	+	Crystal structure of E. coli endonuclease V, an essential enzyme for deamination repair.,Zhang Z, Jia Q, Zhou C, Xie W Sci Rep. 2015 Aug 5;5:12754. doi: 10.1038/srep12754. PMID:26244280<ref>PMID:26244280</ref>

-	~~Authors: Xie~~, W.~~, Zhang, Z~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~The crystal structure of EndoV from E.coli~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deoxyribonuclease V]]
		+	[[Category: Xie, W]]
	[[Category: Zhang, Z]]		[[Category: Zhang, Z]]
-	[[Category: ~~Xie, W~~]]	+	[[Category: Dna repair]]
		+	[[Category: Endonuclease v]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inosine]]
		+	[[Category: Rna cleavage]]

OCA at 14:42, 7 February 2015

OCA — Sat, 07 Feb 2015 14:42:01 GMT

←Older revision		Revision as of 14:42, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xpu is ON HOLD	+	The entry 4xpu is ON HOLD until Jan 18 2017

	Authors: Xie, W., Zhang, Z.		Authors: Xie, W., Zhang, Z.

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

OCA — Wed, 28 Jan 2015 15:40:06 GMT

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

←Older revision

Revision as of 15:40, 28 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xpu is ON HOLD Authors: Xie, W., Zhang, Z. Description: The crystal structure of EndoV from E.coli Category: Unreleased Structures [[Category:...

OCA — Wed, 28 Jan 2015 15:40:05 GMT

New page: '''Unreleased structure''' The entry 4xpu is ON HOLD Authors: Xie, W., Zhang, Z. Description: The crystal structure of EndoV from E.coli Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 4xpu is ON HOLD

Authors: Xie, W., Zhang, Z.

Description: The crystal structure of EndoV from E.coli
[[Category: Unreleased Structures]]
[[Category: Zhang, Z]]
[[Category: Xie, W]]