4muq - Revision history

OCA at 16:42, 20 September 2023

OCA — Wed, 20 Sep 2023 16:42:29 GMT

←Older revision		Revision as of 16:42, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MUQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <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]] 1.364Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [https://pdbe.org/4muq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [https://www.ebi.ac.uk/pdbsum/4muq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4muq 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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [https://pdbe.org/4muq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [https://www.ebi.ac.uk/pdbsum/4muq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4muq ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:11, 28 December 2022

OCA — Wed, 28 Dec 2022 10:11:22 GMT

←Older revision		Revision as of 10:11, 28 December 2022
Line 1:		Line 1:

	==Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog==		==Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog==
-	<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>	+	<StructureSection load='4muq' size='340' side='right'caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MUQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MUQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <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=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [https://pdbe.org/4muq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [https://www.ebi.ac.uk/pdbsum/4muq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4muq ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [~~http~~://pdbe.org/4muq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4muq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4muq ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9KHL8_ENTFL Q9KHL8_ENTFL]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Enterococcus ~~proteiformis thiercelin and jouhaud 1903~~]]	+	[[Category: Enterococcus faecalis]]
-	[[Category: ~~Anderson, W F~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Anderson WF]]
-	[[Category: Courvalin, P]]	+	[[Category: Courvalin P]]
-	[[Category: ~~Evdokimova, E~~]]	+	[[Category: Di Leo R]]
-	[[Category: ~~Leo, R Di~~]]	+	[[Category: Evdokimova E]]
-	[[Category: Meziane-Cherif, D]]	+	[[Category: Meziane-Cherif D]]
-	[[Category: Savchenko, A]]	+	[[Category: Savchenko A]]
-	[[Category: Stogios~~, P J~~]]	+	[[Category: Stogios PJ]]
-	[[Category: Yim, V]]	+	[[Category: Yim V]]
-	~~[[Category: Alpha+beta protein]]~~	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Csgid]]~~	+
-	~~[[Category: D-dipeptidase]]~~	+
-	~~[[Category: Hedgehog/dd-peptidase fold]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Merops m15b subfamily]]~~	+
-	~~[[Category: Metallopeptidase]]~~	+
-	~~[[Category: National institute of allergy and infectious disease]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Vancomycin resistance]]~~	+
-	~~[[Category: Zn2+-dependent d~~]]	+

OCA at 07:55, 11 August 2016

OCA — Thu, 11 Aug 2016 07:55:51 GMT

←Older revision		Revision as of 07:55, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog==		==Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog==
	<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [http://www.ebi.ac.uk/pdbsum/4muq 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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [http://pdbe.org/4muq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [http://www.ebi.ac.uk/pdbsum/4muq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4muq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4muq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:02, 5 January 2015

OCA — Mon, 05 Jan 2015 09:02:52 GMT

←Older revision		Revision as of 09:02, 5 January 2015
Line 2:		Line 2:
	<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>		<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. <br>	+	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MUQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</td></tr>
-	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [http://www.ebi.ac.uk/pdbsum/4muq PDBsum]</span></td></tr>
-	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [http://www.ebi.ac.uk/pdbsum/4muq PDBsum]</span></td></tr>	+	</table>
-	<table>	+
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 14:
	Structural basis for the evolution of vancomycin resistance D,D-peptidases.,Meziane-Cherif D, Stogios PJ, Evdokimova E, Savchenko A, Courvalin P Proc Natl Acad Sci U S A. 2014 Apr 7. PMID:24711382<ref>PMID:24711382</ref>		Structural basis for the evolution of vancomycin resistance D,D-peptidases.,Meziane-Cherif D, Stogios PJ, Evdokimova E, Savchenko A, Courvalin P Proc Natl Acad Sci U S A. 2014 Apr 7. PMID:24711382<ref>PMID:24711382</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]		[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
-	[[Category: Anderson, W F.]]	+	[[Category: Anderson, W F]]
-	[[Category: ~~CSGID, Center for~~ Structural ~~Genomics of Infectious Diseases.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Courvalin, P.]]	+	[[Category: Courvalin, P]]
-	[[Category: Evdokimova, E.]]	+	[[Category: Evdokimova, E]]
-	[[Category: Leo, R Di.]]	+	[[Category: Leo, R Di]]
-	[[Category: Meziane-Cherif, D.]]	+	[[Category: Meziane-Cherif, D]]
-	[[Category: Savchenko, A.]]	+	[[Category: Savchenko, A]]
-	[[Category: Stogios, P J.]]	+	[[Category: Stogios, P J]]
-	[[Category: Yim, V.]]	+	[[Category: Yim, V]]
	[[Category: Alpha+beta protein]]		[[Category: Alpha+beta protein]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
-	[[Category: Center for structural genomics of infectious disease]]
	[[Category: Csgid]]		[[Category: Csgid]]
	[[Category: D-dipeptidase]]		[[Category: D-dipeptidase]]

OCA at 06:43, 14 May 2014

OCA — Wed, 14 May 2014 06:43:30 GMT

←Older revision		Revision as of 06:43, 14 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4muq\| PDB=4muq \| SCENE= }}~~	+	==Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog==
-	===Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog===	+	<StructureSection load='4muq' size='340' side='right' caption='[[4muq]], [[Resolution\|resolution]] 1.36Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24711382}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2D8:(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>2D8</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LY0:(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC+ACID'>LY0</scene>, <scene name='pdbligand=PE3:3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL'>PE3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4f78\|4f78]], [[4mur\|4mur]], [[4mus\|4mus]], [[4mut\|4mut]], [[4oak\|4oak]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vanXYG, vanYG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1351 "Enterococcus proteiformis" Thiercelin and Jouhaud 1903])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4muq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4muq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4muq RCSB], [http://www.ebi.ac.uk/pdbsum/4muq PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vancomycin resistance in Gram-positive bacteria is due to production of cell-wall precursors ending in d-Ala-d-Lac or d-Ala-d-Ser, to which vancomycin exhibits low binding affinities, and to the elimination of the high-affinity precursors ending in d-Ala-d-Ala. Depletion of the susceptible high-affinity precursors is catalyzed by the zinc-dependent d,d-peptidases VanX and VanY acting on dipeptide (d-Ala-d-Ala) or pentapeptide (UDP-MurNac-l-Ala-d-Glu-l-Lys-d-Ala-d-Ala), respectively. Some of the vancomycin resistance operons encode VanXY d,d-carboxypeptidase, which hydrolyzes both di- and pentapeptide. The molecular basis for the diverse specificity of Van d,d-peptidases remains unknown. We present the crystal structures of VanXYC and VanXYG in apo and transition state analog-bound forms and of VanXYC in complex with the d-Ala-d-Ala substrate and d-Ala product. Structural and biochemical analysis identified the molecular determinants of VanXY dual specificity. VanXY residues 110-115 form a mobile cap over the catalytic site, whose flexibility is involved in the switch between di- and pentapeptide hydrolysis. Structure-based alignment of the Van d,d-peptidases showed that VanY enzymes lack this element, which promotes binding of the penta- rather than that of the dipeptide. The structures also highlight the molecular basis for selection of d-Ala-ending precursors over the modified resistance targets. These results illustrate the remarkable adaptability of the d,d-peptidase fold in response to antibiotic pressure via evolution of specific structural elements that confer hydrolytic activity against vancomycin-susceptible peptidoglycan precursors.

-	~~==About this Structure==~~	+	Structural basis for the evolution of vancomycin resistance D,D-peptidases.,Meziane-Cherif D, Stogios PJ, Evdokimova E, Savchenko A, Courvalin P Proc Natl Acad Sci U S A. 2014 Apr 7. PMID:24711382<ref>PMID:24711382</ref>
-	~~[[4muq]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].~~	+

-	==~~Reference~~==	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024711382</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]		[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
	[[Category: Anderson, W F.]]		[[Category: Anderson, W F.]]

OCA at 06:10, 23 April 2014

OCA — Wed, 23 Apr 2014 06:10:07 GMT

←Older revision		Revision as of 06:10, 23 April 2014
Line 1:		Line 1:
	{{STRUCTURE_4muq\| PDB=4muq \| SCENE= }}		{{STRUCTURE_4muq\| PDB=4muq \| SCENE= }}
	===Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog===		===Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog===
		+	{{ABSTRACT_PUBMED_24711382}}

	==About this Structure==		==About this Structure==
	[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].		[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:024711382</ref><references group="xtra"/><references/>
	[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]		[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
	[[Category: Anderson, W F.]]		[[Category: Anderson, W F.]]

OCA at 06:14, 22 January 2014

OCA — Wed, 22 Jan 2014 06:14:17 GMT

←Older revision		Revision as of 06:14, 22 January 2014
Line 3:		Line 3:

	==About this Structure==		==About this Structure==
-	[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterococcus_faecalis Enterococcus faecalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].	+	[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].
-	[[Category: Enterococcus ~~faecalis~~]]	+	[[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]]
	[[Category: Anderson, W F.]]		[[Category: Anderson, W F.]]
	[[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]]		[[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]]

OCA at 06:42, 10 October 2013

OCA — Thu, 10 Oct 2013 06:42:09 GMT

←Older revision		Revision as of 06:42, 10 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4muq\| PDB=4muq \| SCENE= }}
		+	===Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog===

-	~~The entry~~ 4muq is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4muq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MUQ OCA].
-	~~Authors~~: ~~Stogios~~, P.J., Evdokimova, E., Meziane-Cherif, D.~~, Di Leo, R., Yim, V., Courvalin, P.,~~ Savchenko, A., ~~Anderson, W.F~~., Center for ~~Structural Genomics~~ of ~~Infectious Diseases (CSGID)~~	+	[[Category: Enterococcus faecalis]]
-		+	[[Category: Anderson, W F.]]
-	~~Description~~: ~~Crystal Structure of Vancomycin Resistance D,~~D-dipeptidase ~~VanXYg in complex with D~~-~~Ala-D~~-~~Ala phosphinate analog~~	+	[[Category: CSGID, Center for Structural Genomics of Infectious Diseases.]]
		+	[[Category: Courvalin, P.]]
		+	[[Category: Evdokimova, E.]]
		+	[[Category: Leo, R Di.]]
		+	[[Category: Meziane-Cherif, D.]]
		+	[[Category: Savchenko, A.]]
		+	[[Category: Stogios, P J.]]
		+	[[Category: Yim, V.]]
		+	[[Category: Alpha+beta protein]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Center for structural genomics of infectious disease]]
		+	[[Category: Csgid]]
		+	[[Category: D-dipeptidase]]
		+	[[Category: Hedgehog/dd-peptidase fold]]
		+	[[Category: Hydrolase]]
		+	[[Category: Merops m15b subfamily]]
		+	[[Category: Metallopeptidase]]
		+	[[Category: National institute of allergy and infectious disease]]
		+	[[Category: Niaid]]
		+	[[Category: Vancomycin resistance]]
		+	[[Category: Zn2+-dependent d]]

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

OCA — Wed, 02 Oct 2013 06:55:08 GMT

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

←Older revision

Revision as of 06:55, 2 October 2013

OCA: New page: '''Unreleased structure''' The entry 4muq is ON HOLD Authors: Stogios, P.J., Evdokimova, E., Meziane-Cherif, D., Di Leo, R., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Cente...

OCA — Wed, 02 Oct 2013 06:55:07 GMT

New page: '''Unreleased structure''' The entry 4muq is ON HOLD Authors: Stogios, P.J., Evdokimova, E., Meziane-Cherif, D., Di Leo, R., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Cente...

New page

'''Unreleased structure'''

The entry 4muq is ON HOLD

Authors: Stogios, P.J., Evdokimova, E., Meziane-Cherif, D., Di Leo, R., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog