4ly4 - Revision history

OCA at 16:28, 20 September 2023

2023-09-20T16:28:19Z

←Older revision		Revision as of 16:28, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_G27 Helicobacter pylori G27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_G27 Helicobacter pylori G27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.199Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [https://pdbe.org/4ly4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [https://pdbe.org/4ly4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:39, 21 December 2022

2022-12-21T10:39:37Z

←Older revision		Revision as of 10:39, 21 December 2022
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	==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==		==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==
-	<StructureSection load='4ly4' size='340' side='right' caption='[[4ly4]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='4ly4' size='340' side='right'caption='[[4ly4]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Helpg Helpg~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_G27 Helicobacter pylori G27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HP0310, HPG27_289 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])~~</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [https://pdbe.org/4ly4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [https://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [~~http~~://pdbe.org/4ly4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PGDAE_HELPG PGDAE_HELPG] Catalyzes the N-deacetylation of peptidoglycan (PG), an important mechanism that appears to confer lysozyme resistance and to mitigate host immune detection; this likely contributes to pathogen persistence in the host. The exact nature of the residue in PG that is deacetylated has not been determined. Is also able to catalyze the deacetylation of acetylated xylan, and, to a lesser extent, that of chitin and chitosan. Therefore, this enzyme might play a role during infection, considering that xylan-containing carbohydrate structures are among those commonly consumed by humans (By similarity). In vitro, does not show activity on N-acetylglucosamine (GlcNAc), chitotriose (GlcNAc3), some N-acetyl-dipeptides and allantoinase.<ref>PMID:21559431</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: ~~Helpg~~]]	+	[[Category: Helicobacter pylori G27]]
-	[[Category: ~~Shaik, M M~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zanotti, G~~]]	+	[[Category: Shaik MM]]
-	[[Category: ~~Deacetylase]]~~	+	[[Category: Zanotti G]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metallo enzyme]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Peptidoglycan deacetylase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 13:29, 11 August 2016

2016-08-11T13:29:28Z

←Older revision		Revision as of 13:29, 11 August 2016
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		+
	==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==		==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==
	<StructureSection load='4ly4' size='340' side='right' caption='[[4ly4]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='4ly4' size='340' side='right' caption='[[4ly4]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HP0310, HPG27_289 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HP0310, HPG27_289 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [http://www.ebi.ac.uk/pdbsum/4ly4 PDBsum]</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [http://pdbe.org/4ly4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [http://www.ebi.ac.uk/pdbsum/4ly4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ly4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 4ly4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:15, 20 January 2015

2015-01-20T11:15:41Z

←Older revision		Revision as of 11:15, 20 January 2015
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Helpg]]		[[Category: Helpg]]
-	[[Category: Shaik, M M.]]	+	[[Category: Shaik, M M]]
-	[[Category: Zanotti, G.]]	+	[[Category: Zanotti, G]]
	[[Category: Deacetylase]]		[[Category: Deacetylase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 05:26, 8 October 2014

2014-10-08T05:26:34Z

←Older revision		Revision as of 05:26, 8 October 2014
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-	~~{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}~~	+	==Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori==
-	===Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori===	+	<StructureSection load='4ly4' size='340' side='right' caption='[[4ly4]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24346839}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LY4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HP0310, HPG27_289 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=563041 HELPG])</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=4ly4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ly4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ly4 RCSB], [http://www.ebi.ac.uk/pdbsum/4ly4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. In a recent study, we determined the crystallographic structure of the enzyme, which is a homo-tetramer (Shaik et al., PloS One 2011;6:e19207). The metal-binding site, which is essential for the enzyme's catalytic activity, is visible within the structure, but we were unable to identify the nature of the metal itself. In this study, we have obtained a higher-resolution crystal structure of the enzyme, which shows that the ion bound is, in fact, zinc. Analysis of the structure of the four sites, one per monomer, and quantum chemical calculations of models of the site in the presence of different divalent metal ions show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur. Proteins 2014. (c) 2013 Wiley Periodicals, Inc.

-	~~==About this Structure==~~	+	Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.,Munan Shaik M, Bhattacharjee N, Bhattacharjee A, Field MJ, Zanotti G Proteins. 2013 Dec 17. doi: 10.1002/prot.24497. PMID:24346839<ref>PMID:24346839</ref>
-	~~[[4ly4]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Helpg Helpg]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4LY4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024346839</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Helpg]]		[[Category: Helpg]]
	[[Category: Shaik, M M.]]		[[Category: Shaik, M M.]]

OCA at 06:11, 22 January 2014

2014-01-22T06:11:11Z

←Older revision		Revision as of 06:11, 22 January 2014
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	{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}		{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}
	===Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori===		===Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori===
		+	{{ABSTRACT_PUBMED_24346839}}

	==About this Structure==		==About this Structure==
	[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA].		[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024346839</ref><references group="xtra"/><references/>
	[[Category: Helpg]]		[[Category: Helpg]]
	[[Category: Shaik, M M.]]		[[Category: Shaik, M M.]]

OCA at 12:02, 20 November 2013

2013-11-20T12:02:50Z

←Older revision		Revision as of 12:02, 20 November 2013
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	{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}		{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}
-	===Crystal structure of ~~peptidoglyacn deactelyase~~ (HP0310) with Zinc from Helicobacter pylori===	+	===Crystal structure of peptidoglycan deacetylase (HP0310) with Zinc from Helicobacter pylori===

	==About this Structure==		==About this Structure==
-	[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Helicobacter_pylori_g27 Helicobacter pylori g27~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA].	+	[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helpg Helpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA].
-	[[Category: ~~Helicobacter pylori g27~~]]	+	[[Category: Helpg]]
	[[Category: Shaik, M M.]]		[[Category: Shaik, M M.]]
	[[Category: Zanotti, G.]]		[[Category: Zanotti, G.]]

OCA at 07:40, 28 August 2013

2013-08-28T07:40:47Z

←Older revision		Revision as of 07:40, 28 August 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4ly4\| PDB=4ly4 \| SCENE= }}
		+	===Crystal structure of peptidoglyacn deactelyase (HP0310) with Zinc from Helicobacter pylori===

-	~~The entry~~ 4ly4 is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4ly4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori_g27 Helicobacter pylori g27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LY4 OCA].
-	~~Authors~~: Shaik, M.M., Zanotti, G.	+	[[Category: Helicobacter pylori g27]]
-		+	[[Category: Shaik, M M.]]
-	~~Description~~: ~~Crystal structure of peptidoglyacn deactelyase (HP0310) with Zinc from Helicobacter pylori~~	+	[[Category: Zanotti, G.]]
		+	[[Category: Deacetylase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallo enzyme]]
		+	[[Category: Peptidoglycan]]
		+	[[Category: Peptidoglycan deacetylase]]
		+	[[Category: Tim barrel]]

OCA: Protected "4ly4" [edit=sysop:move=sysop]

2013-08-07T20:21:02Z

Protected "4ly4" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:21, 7 August 2013

OCA: New page: '''Unreleased structure''' The entry 4ly4 is ON HOLD Authors: Shaik, M.M., Zanotti, G. Description: Crystal structure of peptidoglyacn deactelyase (HP0310) with Zinc from Helicobacter ...

2013-08-07T20:21:00Z

New page: '''Unreleased structure''' The entry 4ly4 is ON HOLD Authors: Shaik, M.M., Zanotti, G. Description: Crystal structure of peptidoglyacn deactelyase (HP0310) with Zinc from Helicobacter ...

New page

'''Unreleased structure'''

The entry 4ly4 is ON HOLD

Authors: Shaik, M.M., Zanotti, G.

Description: Crystal structure of peptidoglyacn deactelyase (HP0310) with Zinc from Helicobacter pylori