2vgj - Revision history

OCA at 15:19, 13 December 2023

OCA — Wed, 13 Dec 2023 15:19:23 GMT

←Older revision		Revision as of 15:19, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2vgj' size='340' side='right'caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2vgj' size='340' side='right'caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp._R39 Actinomadura sp. R39]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [https://pdbe.org/2vgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [https://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj 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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [https://pdbe.org/2vgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [https://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP] 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 38:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Actinomadura sp]]	+	[[Category: Actinomadura sp. R39]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Charlier P]]
-	[[Category: Charlier, P]]	+	[[Category: Herman R]]
-	[[Category: Herman, R]]	+	[[Category: Sauvage E]]
-	[[Category: Sauvage, E]]	+	[[Category: Kerff F]]
-	[[Category: Kerff, F]]	+
-	~~[[Category: Actinomadura]]~~	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Carboxypeptidase]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall biogenesis/degradation]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Penicillin-binding]]~~	+
-	~~[[Category: Peptidoglycan]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Transpeptidase~~]]	+

OCA at 11:36, 30 March 2022

OCA — Wed, 30 Mar 2022 11:36:50 GMT

←Older revision		Revision as of 11:36, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='2vgj' size='340' side='right'caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2vgj' size='340' side='right'caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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~~://proteopedia.org/fgij/fg.htm?mol=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [~~http~~://pdbe.org/2vgj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj 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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [https://pdbe.org/2vgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [https://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[[https://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP]] 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 07:53, 25 June 2020

OCA — Thu, 25 Jun 2020 07:53:58 GMT

←Older revision		Revision as of 07:53, 25 June 2020
Line 1:		Line 1:

	==Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin==		==Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin==
-	<StructureSection load='2vgj' size='340' side='right' caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='2vgj' size='340' side='right'caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://pdbe.org/2vgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://pdbe.org/2vgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Carboxypeptidase\|Carboxypeptidase]]	+	*[[Carboxypeptidase 3D structures\|Carboxypeptidase 3D structures]]
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Actinomadura sp]]		[[Category: Actinomadura sp]]
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Charlier, P]]		[[Category: Charlier, P]]

OCA at 20:35, 19 September 2018

OCA — Wed, 19 Sep 2018 20:35:24 GMT

←Older revision		Revision as of 20:35, 19 September 2018
Line 1:		Line 1:
-	==~~CRYSTAL STRUCTURE OF ACTINOMADURA~~ R39 DD-~~PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN~~-~~MIMETIC CEPHALOSPORIN~~==	+
		+	==Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin==
	<StructureSection load='2vgj' size='340' side='right' caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2vgj' size='340' side='right' caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://pdbe.org/2vgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj 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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://pdbe.org/2vgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vgj 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/vg/2vgj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vg/2vgj_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 31:		Line 32:

	==See Also==		==See Also==
-	*[[~~Penicillin-binding protein~~\|~~Penicillin-binding protein~~]]	+	*[[Carboxypeptidase\|Carboxypeptidase]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 41:
	[[Category: Charlier, P]]		[[Category: Charlier, P]]
	[[Category: Herman, R]]		[[Category: Herman, R]]
-	[[Category: Kerff, F]]
	[[Category: Sauvage, E]]		[[Category: Sauvage, E]]
		+	[[Category: Kerff, F]]
	[[Category: Actinomadura]]		[[Category: Actinomadura]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]

OCA at 00:57, 10 February 2016

OCA — Wed, 10 Feb 2016 00:57:10 GMT

←Older revision		Revision as of 00:57, 10 February 2016
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj 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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://pdbe.org/2vgj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=2vgj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 2vgj" style="background-color:#fffaf0;"></div>

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

OCA at 10:40, 25 December 2014

OCA — Thu, 25 Dec 2014 10:40:23 GMT

←Older revision		Revision as of 10:40, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj 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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DAC_ACTSP DAC_ACTSP]] 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 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Actinomadura sp.]]	+	[[Category: Actinomadura sp]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Charlier, P.]]	+	[[Category: Charlier, P]]
-	[[Category: Herman, R.]]	+	[[Category: Herman, R]]
-	[[Category: Kerff, F.]]	+	[[Category: Kerff, F]]
-	[[Category: Sauvage, E.]]	+	[[Category: Sauvage, E]]
	[[Category: Actinomadura]]		[[Category: Actinomadura]]
	[[Category: Antibiotic resistance]]		[[Category: Antibiotic resistance]]

OCA at 09:33, 29 September 2014

OCA — Mon, 29 Sep 2014 09:33:28 GMT

←Older revision		Revision as of 09:33, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2vgj.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN==
		+	<StructureSection load='2vgj' size='340' side='right' caption='[[2vgj]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VGJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=REC:CEPHALOSPORIN'>REC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w79\|1w79]], [[1w8q\|1w8q]], [[1w8y\|1w8y]], [[2vgk\|2vgk]]</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=2vgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vgj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vgj RCSB], [http://www.ebi.ac.uk/pdbsum/2vgj 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/vg/2vgj_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 X-ray crystal structures of covalent complexes of the Actinomadura R39 dd-peptidase and Escherichia coli penicillin-binding protein (PBP) 5 with beta-lactams bearing peptidoglycan-mimetic side chains have been determined. The structure of the hydrolysis product of an analogous peptide bound noncovalently to the former enzyme has also been obtained. The R39 DD-peptidase structures reveal the presence of a specific binding site for the D-alpha-aminopimelyl side chain, characteristic of the stem peptide of Actinomadura R39. This binding site features a hydrophobic cleft for the pimelyl methylene groups and strong hydrogen bonding to the polar terminus. Both of these active site elements are provided by amino acid side chains from two separate domains of the protein. In contrast, no clear electron density corresponding to the terminus of the peptidoglycan-mimetic side chains is present when these beta-lactams are covalently bound to PBP5. There is, therefore, no indication of a specific side-chain binding site in this enzyme. These results are in agreement with those from kinetics studies published earlier and support the general prediction made at the time of a direct correlation between kinetics and structural evidence. The essential high-molecular-mass PBPs have demonstrated, to date, no specific reactivity with peptidoglycan-mimetic peptide substrates and beta-lactam inhibitors and, thus, probably do not possess a specific substrate-binding site of the type demonstrated here with the R39 DD-peptidase. This striking deficiency may represent a sophisticated defense mechanism against low-molecular-mass substrate-analogue inhibitors/antibiotics; its discovery should focus new inhibitor design.

-	~~{{STRUCTURE_2vgj\| PDB=2vgj \| SCENE= }}~~	+	Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle.,Sauvage E, Powell AJ, Heilemann J, Josephine HR, Charlier P, Davies C, Pratt RF J Mol Biol. 2008 Aug 29;381(2):383-93. Epub 2008 Jun 10. PMID:18602645<ref>PMID:18602645</ref>

-	~~===CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18602645}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2vgj]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Actinomadura_sp~~. ~~Actinomadura sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ 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:018602645<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Actinomadura sp.]]		[[Category: Actinomadura sp.]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]

OCA at 15:44, 20 October 2012

OCA — Sat, 20 Oct 2012 15:44:51 GMT

←Older revision		Revision as of 15:44, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2vgj]] is a 4 chain structure ~~of [[Carboxypeptidase]] and [[Penicillin-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA].	+	[[2vgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA].

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

OCA: Protected "2vgj" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 19:21:24 GMT

Protected "2vgj" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:21, 26 July 2012

OCA at 19:21, 26 July 2012

OCA — Thu, 26 Jul 2012 19:21:22 GMT

←Older revision		Revision as of 19:21, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2vgj.png\|left\|200px]]		[[Image:2vgj.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2vgj", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2vgj\| PDB=2vgj \| SCENE= }}		{{STRUCTURE_2vgj\| PDB=2vgj \| SCENE= }}

	===CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN===		===CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18602645}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18602645 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18602645}}		{{ABSTRACT_PUBMED_18602645}}

	==About this Structure==		==About this Structure==
-	~~2VGJ~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA].	+	[[2vgj]] is a 4 chain structure of [[Carboxypeptidase]] and [[Penicillin-binding protein]] with sequence from [http://en.wikipedia.org/wiki/Actinomadura_sp. Actinomadura sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VGJ OCA].
		+
		+	==See Also==
		+	*[[Carboxypeptidase\|Carboxypeptidase]]
		+	*[[Penicillin-binding protein\|Penicillin-binding protein]]

	==Reference==		==Reference==
-	Crystal structures of complexes of bacterial DD-peptidases with peptidoglycan-mimetic ligands: the substrate specificity puzzle., Sauvage E, Powell AJ, Heilemann J, Josephine HR, Charlier P, Davies C, Pratt RF, J Mol Biol. 2008 Aug 29;381(2):383-93. Epub 2008 Jun 10. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18602645 18602645]~~	+	<ref group="xtra">PMID:018602645</ref><references group="xtra"/>
	[[Category: Actinomadura sp.]]		[[Category: Actinomadura sp.]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
Line 42:		Line 34:
	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Transpeptidase]]		[[Category: Transpeptidase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Dec 5 09:55:32 2008''