1nzu - Revision history

OCA at 09:27, 16 August 2023

2023-08-16T09:27:44Z

←Older revision		Revision as of 09:27, 16 August 2023
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	<StructureSection load='1nzu' size='340' side='right'caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nzu' size='340' side='right'caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NZU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BME:BETA~~-~~MERCAPTOETHANOL'>BME</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]] 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;'>[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [https://pdbe.org/1nzu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [https://www.ebi.ac.uk/pdbsum/1nzu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzu ProSAT]</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~~://proteopedia.org/fgij/fg.htm?mol=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [~~http~~://pdbe.org/1nzu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nzu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DACA_ECOLI DACA_ECOLI]] Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.	+	[https://www.uniprot.org/uniprot/DACA_ECOLI DACA_ECOLI] 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]~~	+	[[Category: Davies C]]
-	[[Category: Davies, C]]	+	[[Category: Nicholas RA]]
-	[[Category: Nicholas~~, R A~~]]	+	[[Category: Nicola G]]
-	[[Category: Nicola, G]]	+
-	~~[[Category: Dd-carboxypeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Penicillin-binding protein]]~~	+
-	~~[[Category: Peptidoglycan synthesis~~]]	+

OCA at 09:01, 2 December 2020

2020-12-02T09:01:01Z

←Older revision		Revision as of 09:01, 2 December 2020
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	==Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol==		==Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol==
-	<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1nzu' size='340' side='right'caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NZU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://pdbe.org/1nzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzu 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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://pdbe.org/1nzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1nzu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nzu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Penicillin-binding protein 3D structures\|Penicillin-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Davies, C]]		[[Category: Davies, C]]

OCA at 07:31, 7 February 2018

2018-02-07T07:31:55Z

←Older revision		Revision as of 07:31, 7 February 2018
Line 1:		Line 1:
		+
	==Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol==		==Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol==
	<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://pdbe.org/1nzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu 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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://pdbe.org/1nzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nzu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nz/1nzu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nz/1nzu_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>
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	</div>		</div>
	<div class="pdbe-citations 1nzu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nzu" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Penicillin-binding protein\|Penicillin-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:57, 10 February 2016

2016-02-10T06:57:09Z

←Older revision		Revision as of 06:57, 10 February 2016
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	<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=1nzu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:28, 11 September 2015

2015-09-11T06:28:40Z

←Older revision		Revision as of 06:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu 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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://pdbe.org/1nzu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1nzu" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
	[[Category: Davies, C]]		[[Category: Davies, C]]

OCA at 12:35, 25 December 2014

2014-12-25T12:35:12Z

←Older revision		Revision as of 12:35, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu 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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DACA_ECOLI DACA_ECOLI]] 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 36:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-	[[Category: Davies, C.]]	+	[[Category: Davies, C]]
-	[[Category: Nicholas, R A.]]	+	[[Category: Nicholas, R A]]
-	[[Category: Nicola, G.]]	+	[[Category: Nicola, G]]
	[[Category: Dd-carboxypeptidase]]		[[Category: Dd-carboxypeptidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Penicillin-binding protein]]		[[Category: Penicillin-binding protein]]
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]

OCA at 14:40, 28 September 2014

2014-09-28T14:40:01Z

←Older revision		Revision as of 14:40, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1nzu.~~png~~\|~~left~~\|200px]]	+	==Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol==
		+	<StructureSection load='1nzu' size='340' side='right' caption='[[1nzu]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nzu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NZU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1hd8\|1hd8]], [[1nj4\|1nj4]], [[1nzo\|1nzo]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DACA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=1nzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nzu RCSB], [http://www.ebi.ac.uk/pdbsum/1nzu 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/nz/1nzu_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 ==
		+	Penicillin-binding proteins (PBPs), which are the lethal targets of beta-lactam antibiotics, catalyse the final stages of peptidoglycan biosynthesis of the bacterial cell wall. PBP 5 of Escherichia coli is a D-alanine CPase (carboxypeptidase) that has served as a useful model to elucidate the catalytic mechanism of low-molecular-mass PBPs. Previous studies have shown that modification of Cys115 with a variety of reagents results in a loss of CPase activity and a large decrease in the rate of deacylation of the penicilloyl-PBP 5 complex [Tamura, Imae and Strominger (1976) J. Biol. Chem. 251, 414-423; Curtis and Strominger (1978) J. Biol. Chem. 253, 2584-2588]. The crystal structure of wild-type PBP 5 in which Cys115 fortuitously had formed a covalent adduct with 2-mercaptoethanol was solved at 2.0 A (0.2 nm) resolution, and these results provide a structural rationale for how thiol-directed reagents lower the rate of deacylation. When compared with the structure of the unmodified wild-type enzyme, a major change in the architecture of the active site is observed. The two largest differences are the disordering of a loop comprising residues 74-90 and a shift in residues 106-111, which results in the displacement of Ser110 of the SXN active-site motif. These results support the developing hypothesis that the SXN motif of PBP 5, and especially Ser110, is intimately involved in the catalytic mechanism of deacylation.

-	~~{{STRUCTURE_1nzu\| PDB=1nzu \| SCENE= }}~~	+	A large displacement of the SXN motif of Cys115-modified penicillin-binding protein 5 from Escherichia coli.,Nicola G, Fedarovich A, Nicholas RA, Davies C Biochem J. 2005 Nov 15;392(Pt 1):55-63. PMID:16038617<ref>PMID:16038617</ref>

-	~~===Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16038617}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1nzu]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU 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:016038617<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]

OCA at 16:43, 20 October 2012

2012-10-20T16:43:54Z

←Older revision		Revision as of 16:43, 20 October 2012
Line 8:		Line 8:

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

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

OCA: Protected "1nzu" [edit=sysop:move=sysop]

2012-07-26T22:39:36Z

Protected "1nzu" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:39, 26 July 2012

OCA at 22:39, 26 July 2012

2012-07-26T22:39:35Z

←Older revision		Revision as of 22:39, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1nzu.png\|left\|200px]]		[[Image:1nzu.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nzu", 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_1nzu\| PDB=1nzu \| SCENE= }}		{{STRUCTURE_1nzu\| PDB=1nzu \| SCENE= }}

	===Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol===		===Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16038617}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16038617 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16038617}}		{{ABSTRACT_PUBMED_16038617}}

	==About this Structure==		==About this Structure==
-	~~1NZU~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA].	+	[[1nzu]] is a 1 chain structure of [[Carboxypeptidase]] and [[Penicillin-binding protein]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NZU OCA].
		+
		+	==See Also==
		+	*[[Carboxypeptidase\|Carboxypeptidase]]
		+	*[[Penicillin-binding protein\|Penicillin-binding protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16038617~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016038617</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]		[[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
Line 33:		Line 25:
	[[Category: Penicillin-binding protein]]		[[Category: Penicillin-binding protein]]
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:19:09 2009''