5cms - Revision history

OCA at 16:10, 8 November 2023

2023-11-08T16:10:04Z

← Older revision		Revision as of 16:10, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cms]] is a 18 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=5CMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cms]] is a 18 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=5CMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.98Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [https://pdbe.org/5cms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [https://www.ebi.ac.uk/pdbsum/5cms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cms 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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [https://pdbe.org/5cms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [https://www.ebi.ac.uk/pdbsum/5cms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cms ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:17, 14 June 2023

2023-06-14T12:17:02Z

← Older revision		Revision as of 12:17, 14 June 2023
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	==Structural Insights into the Mechanism of Escherichia coli Ymdb==		==Structural Insights into the Mechanism of Escherichia coli Ymdb==
	<StructureSection load='5cms' size='340' side='right' caption='[[5cms]], [[Resolution\|resolution]] 2.98Å' scene=''>		<StructureSection load='5cms' size='340' side='right'caption='[[5cms]], [[Resolution\|resolution]] 2.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cms]] is a 18 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=5CMS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CMS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cms]] is a 18 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=5CMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CMS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ymdB ([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'>[https://proteopedia.org/fgij/fg.htm?mol=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [https://pdbe.org/5cms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [https://www.ebi.ac.uk/pdbsum/5cms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cms 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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [~~http~~://pdbe.org/5cms PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cms PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cms ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/~~C3TEL7_ECOLX C3TEL7_ECOLX]~~] Deacetylates O-acetyl-ADP ribose. Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation.~~[HAMAP-Rule~~:~~MF_01205]~~		[https://www.uniprot.org/uniprot/YMDB_ECOLI YMDB_ECOLI] Deacetylates O-acetyl-ADP ribose. Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation.<ref>PMID:19141481</ref> <ref>PMID:21257746</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: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Shao, C]]		[[Category: Large Structures]]
	[[Category: Song, Y]]		[[Category: Shao C]]
	[[Category: Wang, C]]		[[Category: Song Y]]
	[[Category: Zang, J]]		[[Category: Wang C]]
	[[Category: Zhang, W]]		[[Category: Zang J]]
	[[Category: Zhang, X]]		[[Category: Zhang W]]
	~~[[Category: Adpr]]~~		[[Category: Zhang X]]
	~~[[Category: Deacetylase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Macro domain]]~~
	~~[[Category: Oaadpr~~]]

OCA at 12:28, 6 November 2017

2017-11-06T12:28:32Z

← Older revision		Revision as of 12:28, 6 November 2017
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	==Structural Insights into the Mechanism of Escherichia coli Ymdb==		==Structural Insights into the Mechanism of Escherichia coli Ymdb==
	<StructureSection load='5cms' size='340' side='right' caption='[[5cms]], [[Resolution\|resolution]] 2.98Å' scene=''>		<StructureSection load='5cms' size='340' side='right' caption='[[5cms]], [[Resolution\|resolution]] 2.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cms]] is a 18 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMS FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cms]] is a 18 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=5CMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [http://pdbe.org/5cms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [http://www.ebi.ac.uk/pdbsum/5cms PDBsum]</span></td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ymdB ([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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [http://pdbe.org/5cms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [http://www.ebi.ac.uk/pdbsum/5cms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cms ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus coli migula 1895]]
	[[Category: Shao, C]]		[[Category: Shao, C]]
	[[Category: Song, Y]]		[[Category: Song, Y]]

OCA at 10:05, 2 December 2015

2015-12-02T10:05:26Z

← Older revision		Revision as of 10:05, 2 December 2015
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	'''~~Unreleased~~ structure'''		==Structural Insights into the Mechanism of Escherichia coli Ymdb==
			<StructureSection load='5cms' size='340' side='right' caption='[[5cms]], [[Resolution\|resolution]] 2.98Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[5cms]] is a 18 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CMS FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5cms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cms OCA], [http://pdbe.org/5cms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cms RCSB], [http://www.ebi.ac.uk/pdbsum/5cms PDBsum]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/C3TEL7_ECOLX C3TEL7_ECOLX]] Deacetylates O-acetyl-ADP ribose. Down-regulates ribonuclease 3 (RNase III) activity. Acts by interacting directly with the region of the ribonuclease that is required for dimerization/activation.[HAMAP-Rule:MF_01205]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The Escherichia coli protein YmdB belongs to the macrodomain protein family, which can bind ADP-ribose (ADPr) and its derivatives. Recently, YmdB was reported to be capable of deacetylating O-acetyl-ADP-ribose (OAADPr) to yield ADPr and free acetate. To study the substrate specificity and catalytic mechanism, the crystal structures of E. coli YmdB in complex with ADPr, double mutant N25AD35A complexed with 2'-OAADPr, and Y126A/ADPr complex were solved at 1.8A, 2.8A and 3.0A resolution, respectively. Structural and biochemical studies reveal that YmdB has substrate specificity against 2'-OAADPr. The conserved residues Asn25 and Asp35 are crucial for catalytic activity, and an active water molecule is proposed as the nucleophile to attack the acetyl group of 2'-OAADPr. Our findings indicate that the conserved phenyl group of Tyr126 plays a crucial role in catalytic activity by stabilizing the right orientation of distal ribose and that Gly32 may be important for activity by interacting with the acetyl group of 2'-OAADPr. Based on these observations, a model of YmdB in complex with 2'-OAADPr was made to illustrate the proposed catalytic mechanism of YmdB.

	~~The entry 5cms is ON HOLD until Paper Publication~~		Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase.,Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419<ref>PMID:26481419</ref>

	~~Authors: Zhang~~, W.~~, Wang, C~~.~~, Song, Y~~., Shao, C., ~~Zhang, X., Zang, J.~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description~~: ~~Structural Insights into the Mechanism of Escherichia coli Ymdb~~		<div class="pdbe-citations 5cms" style="background-color:#fffaf0;"></div>
	[[Category: ~~Unreleased Structures~~]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Shao, C]]
			[[Category: Song, Y]]
			[[Category: Wang, C]]
			[[Category: Zang, J]]
	[[Category: Zhang, W]]		[[Category: Zhang, W]]
	[[Category: Zhang, X]]		[[Category: Zhang, X]]
	[[Category: ~~Song, Y~~]]		[[Category: Adpr]]
	[[Category: ~~Zang, J~~]]		[[Category: Deacetylase]]
	[[Category: ~~Shao, C~~]]		[[Category: Hydrolase]]
	[[Category: ~~Wang, C~~]]		[[Category: Macro domain]]
			[[Category: Oaadpr]]

OCA at 18:43, 5 August 2015

2015-08-05T18:43:48Z

← Older revision		Revision as of 18:43, 5 August 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 5cms is ON HOLD		The entry 5cms is ON HOLD until Paper Publication

	Authors: Zhang, W., Wang, C., Song, Y., Shao, C., Zhang, X., Zang, J.		Authors: Zhang, W., Wang, C., Song, Y., Shao, C., Zhang, X., Zang, J.

OCA at 13:34, 29 July 2015

2015-07-29T13:34:55Z

← Older revision		Revision as of 13:34, 29 July 2015
Line 3:		Line 3:
	The entry 5cms is ON HOLD		The entry 5cms is ON HOLD

	Authors: ~~Weichang~~ Zhang, ~~Chengliang~~ Wang, ~~Yang~~ Song, ~~Chen~~ Shao, ~~Xuan~~ Zhang, ~~Jianye~~ Zang		Authors: Zhang, W., Wang, C., Song, Y., Shao, C., Zhang, X., Zang, J.

	Description: Structural Insights into the Mechanism of Escherichia coli Ymdb		Description: Structural Insights into the Mechanism of Escherichia coli Ymdb
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: ~~Weichang~~ Zhang, ~~Chengliang Wang~~, ~~Yang~~ Song, ~~Chen~~ Shao, ~~Xuan Zhang~~, ~~Jianye Zang~~]]		[[Category: Zhang, W]]
			[[Category: Zhang, X]]
			[[Category: Song, Y]]
			[[Category: Zang, J]]
			[[Category: Shao, C]]
			[[Category: Wang, C]]

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

2015-07-22T13:22:01Z

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

← Older revision	Revision as of 13:22, 22 July 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5cms is ON HOLD Authors: Weichang Zhang, Chengliang Wang, Yang Song, Chen Shao, Xuan Zhang, Jianye Zang Description: Structural Insights into the M...

2015-07-22T13:22:00Z

New page: '''Unreleased structure''' The entry 5cms is ON HOLD Authors: Weichang Zhang, Chengliang Wang, Yang Song, Chen Shao, Xuan Zhang, Jianye Zang Description: Structural Insights into the M...

New page

'''Unreleased structure'''

The entry 5cms is ON HOLD

Authors: Weichang Zhang, Chengliang Wang, Yang Song, Chen Shao, Xuan Zhang, Jianye Zang

Description: Structural Insights into the Mechanism of Escherichia coli Ymdb
[[Category: Unreleased Structures]]
[[Category: Weichang Zhang, Chengliang Wang, Yang Song, Chen Shao, Xuan Zhang, Jianye Zang]]