3zgp - Revision history

OCA at 10:06, 14 June 2023

2023-06-14T10:06:55Z

←Older revision		Revision as of 10:06, 14 June 2023
Line 1:		Line 1:

	==NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem==		==NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem==
-	<StructureSection load='3zgp' size='340' side='right'caption='[[3zgp~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='3zgp' size='340' side='right'caption='[[3zgp]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_19434 Atcc 19434~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zg4\|3zg4]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidyltransferase Peptidyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.12 2.3.2.12] </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=3zgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgp OCA], [https://pdbe.org/3zgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zgp RCSB], [https://www.ebi.ac.uk/pdbsum/3zgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgp 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=3zgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgp OCA], [https://pdbe.org/3zgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zgp RCSB], [https://www.ebi.ac.uk/pdbsum/3zgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q3Y185_ENTFD Q3Y185_ENTFD]
	<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: ~~Atcc 19434~~]]	+	[[Category: Enterococcus faecium]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peptidyltransferase]]~~	+	[[Category: Arthur M]]
-	[[Category: Arthur, M]]	+	[[Category: Bougault C]]
-	[[Category: Bougault, C]]	+	[[Category: Dubee V]]
-	[[Category: Dubee, V]]	+	[[Category: Hugonnet JE]]
-	[[Category: Hugonnet~~, J E~~]]	+	[[Category: Lecoq L]]
-	[[Category: Lecoq, L]]	+	[[Category: Simorre JP]]
-	[[Category: Simorre~~, J P~~]]	+	[[Category: Triboulet S]]
-	[[Category: Triboulet, S]]	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Peptidoglycan biosynthesis]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transpeptidation~~]]	+

OCA at 05:46, 10 August 2022

2022-08-10T05:46:11Z

←Older revision		Revision as of 05:46, 10 August 2022
Line 3:		Line 3:
	<StructureSection load='3zgp' size='340' side='right'caption='[[3zgp]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='3zgp' size='340' side='right'caption='[[3zgp]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zg4\|3zg4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zg4\|3zg4]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptidyltransferase Peptidyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.12 2.3.2.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidyltransferase Peptidyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.12 2.3.2.12] </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=3zgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgp OCA], [~~http~~://pdbe.org/3zgp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zgp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zgp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgp 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=3zgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgp OCA], [https://pdbe.org/3zgp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zgp RCSB], [https://www.ebi.ac.uk/pdbsum/3zgp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 12:49, 1 January 2020

2020-01-01T12:49:26Z

←Older revision		Revision as of 12:49, 1 January 2020
Line 1:		Line 1:

	==NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem==		==NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem==
-	<StructureSection load='3zgp' size='340' side='right' caption='[[3zgp]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='3zgp' size='340' side='right'caption='[[3zgp]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 19434]]		[[Category: Atcc 19434]]
		+	[[Category: Large Structures]]
	[[Category: Peptidyltransferase]]		[[Category: Peptidyltransferase]]
	[[Category: Arthur, M]]		[[Category: Arthur, M]]

OCA at 15:10, 11 August 2016

2016-08-11T15:10:10Z

←Older revision		Revision as of 15:10, 11 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_3zgp\| PDB=3zgp \| SCENE= }}
-	===NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem===
-	{{ABSTRACT_PUBMED_23574509}}

-	==~~About this Structure~~==	+	==NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem==
-	[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].	+	<StructureSection load='3zgp' size='340' side='right' caption='[[3zgp]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZGP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1RG:(4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL)CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC+ACID'>1RG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zg4\|3zg4]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidyltransferase Peptidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.2.12 2.3.2.12] </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=3zgp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zgp OCA], [http://pdbe.org/3zgp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zgp RCSB], [http://www.ebi.ac.uk/pdbsum/3zgp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zgp ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a biopolymer highly cross-linked through d,d-transpeptidation. Peptidoglycan cross-linking is catalyzed by penicillin-binding proteins (PBPs) that are the essential target of beta-lactam antibiotics. PBPs are functionally replaced by l,d-transpeptidases (Ldts) in ampicillin-resistant mutants of Enterococcus faecium and in wild-type Mycobacterium tuberculosis. Ldts are inhibited in vivo by a single class of beta-lactams, the carbapenems, which act as a suicide substrate. We present here the first structure of a carbapenem-acylated l,d-transpeptidase, E. faecium Ldtfm acylated by ertapenem, which revealed key contacts between the carbapenem core and residues of the catalytic cavity of the enzyme. Significant reorganization of the antibiotic conformation occurs upon enzyme acylation. These results, together with the analysis of protein-to-carbapenem proton transfers, provide new insights into the mechanism of Ldt acylation by carbapenems.

-	~~==Reference==~~	+	Structure of Enterococcus faeciuml,d-Transpeptidase Acylated by Ertapenem Provides Insight into the Inactivation Mechanism.,Lecoq L, Dubee V, Triboulet S, Bougault C, Hugonnet JE, Arthur M, Simorre JP ACS Chem Biol. 2013 Apr 12. PMID:23574509<ref>PMID:23574509</ref>
-	<ref ~~group="xtra"~~>PMID:~~023574509~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3zgp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 19434]]		[[Category: Atcc 19434]]
	[[Category: Peptidyltransferase]]		[[Category: Peptidyltransferase]]
-	[[Category: Arthur, M.]]	+	[[Category: Arthur, M]]
-	[[Category: Bougault, C.]]	+	[[Category: Bougault, C]]
-	[[Category: Dubee, V.]]	+	[[Category: Dubee, V]]
-	[[Category: Hugonnet, J E.]]	+	[[Category: Hugonnet, J E]]
-	[[Category: Lecoq, L.]]	+	[[Category: Lecoq, L]]
-	[[Category: Simorre, J P.]]	+	[[Category: Simorre, J P]]
-	[[Category: Triboulet, S.]]	+	[[Category: Triboulet, S]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]
	[[Category: Peptidoglycan biosynthesis]]		[[Category: Peptidoglycan biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Transpeptidation]]		[[Category: Transpeptidation]]

OCA at 03:54, 13 February 2014

2014-02-13T03:54:17Z

←Older revision		Revision as of 03:54, 13 February 2014
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterococcus_faecium Enterococcus faecium~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].	+	[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19434 Atcc 19434]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023574509</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023574509</ref><references group="xtra"/><references/>
-	[[Category: ~~Enterococcus faecium~~]]	+	[[Category: Atcc 19434]]
	[[Category: Peptidyltransferase]]		[[Category: Peptidyltransferase]]
	[[Category: Arthur, M.]]		[[Category: Arthur, M.]]

OCA at 05:20, 28 August 2013

2013-08-28T05:20:29Z

←Older revision		Revision as of 05:20, 28 August 2013
Line 5:		Line 5:
	==About this Structure==		==About this Structure==
	[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].		[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023574509</ref><references group="xtra"/><references/>
	[[Category: Enterococcus faecium]]		[[Category: Enterococcus faecium]]
	[[Category: Peptidyltransferase]]		[[Category: Peptidyltransferase]]

OCA at 11:22, 24 April 2013

2013-04-24T11:22:45Z

←Older revision		Revision as of 11:22, 24 April 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3zgp\| PDB=3zgp \| SCENE= }}
		+	===NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem===
		+	{{ABSTRACT_PUBMED_23574509}}

-	~~The entry~~ 3zgp is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3zgp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterococcus_faecium Enterococcus faecium]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZGP OCA].
-	~~Authors~~: ~~Lecoq~~, L., ~~Triboulet, S~~., Dubee, V.~~, Bougault, C.,~~ Hugonnet, J.E., ~~Arthur, M~~., Simorre, J.P.	+	[[Category: Enterococcus faecium]]
-		+	[[Category: Peptidyltransferase]]
-	~~Description~~: ~~NMR structure of the catalytic domain from E. faecium L~~,~~D-transpeptidase acylated by ertapenem~~	+	[[Category: Arthur, M.]]
		+	[[Category: Bougault, C.]]
		+	[[Category: Dubee, V.]]
		+	[[Category: Hugonnet, J E.]]
		+	[[Category: Lecoq, L.]]
		+	[[Category: Simorre, J P.]]
		+	[[Category: Triboulet, S.]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Peptidoglycan biosynthesis]]
		+	[[Category: Transferase]]
		+	[[Category: Transpeptidation]]

OCA: Protected "3zgp" [edit=sysop:move=sysop]

2013-01-02T08:39:41Z

Protected "3zgp" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:39, 2 January 2013

OCA: New page: '''Unreleased structure''' The entry 3zgp is ON HOLD until Paper Publication Authors: Lecoq, L., Triboulet, S., Dubee, V., Bougault, C., Hugonnet, J.E., Arthur, M., Simorre, J.P. Descr...

2013-01-02T08:39:40Z

New page: '''Unreleased structure''' The entry 3zgp is ON HOLD until Paper Publication Authors: Lecoq, L., Triboulet, S., Dubee, V., Bougault, C., Hugonnet, J.E., Arthur, M., Simorre, J.P. Descr...

New page

'''Unreleased structure'''

The entry 3zgp is ON HOLD until Paper Publication

Authors: Lecoq, L., Triboulet, S., Dubee, V., Bougault, C., Hugonnet, J.E., Arthur, M., Simorre, J.P.

Description: NMR structure of the catalytic domain from E. faecium L,D-transpeptidase acylated by ertapenem