1es3 - Revision history

OCA at 07:06, 7 February 2024

2024-02-07T07:06:24Z

←Older revision		Revision as of 07:06, 7 February 2024
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	<StructureSection load='1es3' size='340' side='right'caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1es3' size='340' side='right'caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Strsk Strsk~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._K15 Streptomyces sp. K15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </~~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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [https://pdbe.org/1es3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [https://www.ebi.ac.uk/pdbsum/1es3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [https://pdbe.org/1es3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [https://www.ebi.ac.uk/pdbsum/1es3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1es3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[https://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1es3 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1es3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis. The Lys38His and Ser96Ala mutations almost completely abolished the penicillin binding and severely impaired the transpeptidase activities while the geometry of the active site was essentially the same as in the wild-type enzyme. It is proposed that Lys38 acts as the catalytic base that abstracts a proton from the active serine Ser35 during nucleophilic attack and that Ser96 is a key intermediate in the proton transfer from the Ogamma of Ser35 to the substrate leaving group nitrogen. The role of these two residues should be conserved among penicillin-binding proteins containing the Ser-Xaa-Asn/Cys sequence in motif 2. Conversion of Cys98 into Asn decreased the transpeptidase activity and increased hydrolysis of the thiolester substrate and the acylation rate with most beta-lactam antibiotics. Cys98 is proposed to play the same role as Asn in motif 2 of other penicilloyl serine transferases in properly positioning the substrate for the catalytic process.
-
-	Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.,Rhazi N, Charlier P, Dehareng D, Engher D, Vermeire M, Frere JM, Nguyen-Disteche M, Fonze E Biochemistry. 2003 Mar 18;42(10):2895-906. PMID:12627955<ref>PMID:12627955</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1es3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]		*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]		*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Streptomyces sp. K15]]
-	~~[[Category: Strsk~~]]	+	[[Category: Charlier P]]
-	[[Category: Charlier, P]]	+	[[Category: Fonze E]]
-	[[Category: Fonze, E]]	+
-	~~[[Category: Beta-lactamase]]~~	+
-	~~[[Category: Dd-transpeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase carboxypeptidase]]~~	+
-	~~[[Category: Penicillin-binding]]~~	+
-	~~[[Category: Serine peptidase~~]]	+

OCA at 09:41, 21 July 2021

2021-07-21T09:41:03Z

←Older revision		Revision as of 09:41, 21 July 2021
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	<StructureSection load='1es3' size='340' side='right'caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1es3' size='340' side='right'caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Strsk Strsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Strsk Strsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [~~http~~://pdbe.org/1es3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1es3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [https://pdbe.org/1es3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [https://www.ebi.ac.uk/pdbsum/1es3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1es3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[[https://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	==See Also==		==See Also==
	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]		*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:31, 16 October 2019

2019-10-16T10:31:49Z

←Older revision		Revision as of 10:31, 16 October 2019
Line 1:		Line 1:

	==C98A mutant of streptomyces K15 DD-transpeptidase==		==C98A mutant of streptomyces K15 DD-transpeptidase==
-	<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1es3' size='340' side='right'caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsk Strsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsk Strsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1es3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1es3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Strsk]]		[[Category: Strsk]]

OCA at 07:12, 20 December 2017

2017-12-20T07:12:18Z

←Older revision		Revision as of 07:12, 20 December 2017
Line 1:		Line 1:
		+
	==C98A mutant of streptomyces K15 DD-transpeptidase==		==C98A mutant of streptomyces K15 DD-transpeptidase==
	<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://pdbe.org/1es3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://pdbe.org/1es3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1es3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/1es3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/1es3_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1es3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1es3" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:29, 7 February 2016

2016-02-07T06:29:53Z

←Older revision		Revision as of 06:29, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1es3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:44, 9 September 2015

2015-09-09T22:44:33Z

←Older revision		Revision as of 22:44, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_sp. Streptomyces sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsk Strsk]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://pdbe.org/1es3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1es3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: ~~Streptomyces sp~~]]	+	[[Category: Strsk]]
	[[Category: Charlier, P]]		[[Category: Charlier, P]]
	[[Category: Fonze, E]]		[[Category: Fonze, E]]

OCA at 08:38, 24 December 2014

2014-12-24T08:38:08Z

←Older revision		Revision as of 08:38, 24 December 2014
Line 8:		Line 8:
	<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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DACX_STRSK DACX_STRSK]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 20:16, 22 December 2014

2014-12-22T20:16:31Z

←Older revision		Revision as of 20:16, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Streptomyces sp.]]	+	[[Category: Streptomyces sp]]
-	[[Category: Charlier, P.]]	+	[[Category: Charlier, P]]
-	[[Category: Fonze, E.]]	+	[[Category: Fonze, E]]
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
	[[Category: Dd-transpeptidase]]		[[Category: Dd-transpeptidase]]

OCA at 11:22, 24 September 2014

2014-09-24T11:22:53Z

←Older revision		Revision as of 11:22, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1es3.~~png~~\|~~left~~\|200px]]	+	==C98A mutant of streptomyces K15 DD-transpeptidase==
		+	<StructureSection load='1es3' size='340' side='right' caption='[[1es3]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ES3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1skf\|1skf]], [[1eqs\|1eqs]], [[1es2\|1es2]], [[1es4\|1es4]], [[1es5\|1es5]], [[1esi\|1esi]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=1es3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1es3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1es3 RCSB], [http://www.ebi.ac.uk/pdbsum/1es3 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/1es3_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Streptomyces K15 penicillin-binding DD-transpeptidase is presumed to be involved in peptide cross-linking during bacterial cell wall peptidoglycan assembly. To gain insight into the catalytic mechanism, the roles of residues Lys38, Ser96, and Cys98, belonging to the structural elements defining the active site cleft, have been investigated by site-directed mutagenesis, biochemical studies, and X-ray diffraction analysis. The Lys38His and Ser96Ala mutations almost completely abolished the penicillin binding and severely impaired the transpeptidase activities while the geometry of the active site was essentially the same as in the wild-type enzyme. It is proposed that Lys38 acts as the catalytic base that abstracts a proton from the active serine Ser35 during nucleophilic attack and that Ser96 is a key intermediate in the proton transfer from the Ogamma of Ser35 to the substrate leaving group nitrogen. The role of these two residues should be conserved among penicillin-binding proteins containing the Ser-Xaa-Asn/Cys sequence in motif 2. Conversion of Cys98 into Asn decreased the transpeptidase activity and increased hydrolysis of the thiolester substrate and the acylation rate with most beta-lactam antibiotics. Cys98 is proposed to play the same role as Asn in motif 2 of other penicilloyl serine transferases in properly positioning the substrate for the catalytic process.

-	~~{{STRUCTURE_1es3\| PDB=1es3 \| SCENE= }}~~	+	Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.,Rhazi N, Charlier P, Dehareng D, Engher D, Vermeire M, Frere JM, Nguyen-Disteche M, Fonze E Biochemistry. 2003 Mar 18;42(10):2895-906. PMID:12627955<ref>PMID:12627955</ref>

-	~~===C98A mutant~~ of ~~streptomyces K15 DD-transpeptidase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12627955}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1es3]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_sp~~. ~~Streptomyces sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA].~~	+

	==See Also==		==See Also==
-	*[[Carboxypeptidase\|Carboxypeptidase]]
	*[[Penicillin-binding protein\|Penicillin-binding protein]]		*[[Penicillin-binding protein\|Penicillin-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012627955<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Streptomyces sp.]]		[[Category: Streptomyces sp.]]

OCA at 05:51, 20 October 2012

2012-10-20T05:51:19Z

←Older revision		Revision as of 05:51, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1es3]] is a 1 chain structure ~~of [[Carboxypeptidase]] and [[Penicillin-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA].	+	[[1es3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ES3 OCA].

	==See Also==		==See Also==