3b8u - Revision history

OCA at 14:42, 1 November 2023

OCA — Wed, 01 Nov 2023 14:42:30 GMT

←Older revision		Revision as of 14:42, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3b8u' size='340' side='right'caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3b8u' size='340' side='right'caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b8u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b8u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PLP:PYRIDOXAL~~-~~5-PHOSPHATE'>PLP</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]] 3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">alr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>~~	+
-	~~<tr id='activity~~'>~~<td class="sblockLbl"><b>Activity:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [https://pdbe.org/3b8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [https://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u 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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [https://pdbe.org/3b8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [https://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>	+	[https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>
	== 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: ~~Alanine racemase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hu, T]]	+	[[Category: Hu T]]
-	[[Category: Jiang, H]]	+	[[Category: Jiang H]]
-	[[Category: Shen, X]]	+	[[Category: Shen X]]
-	[[Category: Wu, D]]	+	[[Category: Wu D]]
-	[[Category: Zhang, L]]	+	[[Category: Zhang L]]
-	~~[[Category: Alpha/beta barrel]]~~	+
-	~~[[Category: Cell shape]]~~	+
-	~~[[Category: Cell wall biogenesis/degradation]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Peptidoglycan synthesis]]~~	+
-	~~[[Category: Pyridoxal phosphate~~]]	+

OCA at 07:25, 10 November 2021

OCA — Wed, 10 Nov 2021 07:25:42 GMT

←Older revision		Revision as of 07:25, 10 November 2021
Line 1:		Line 1:

	==Crystal structure of Escherichia coli alaine racemase mutant E221A==		==Crystal structure of Escherichia coli alaine racemase mutant E221A==
-	<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='3b8u' size='340' side='right'caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b8u]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3B8U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b8u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [~~http~~://pdbe.org/3b8u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u 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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [https://pdbe.org/3b8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [https://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>	+	[[https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:

	==See Also==		==See Also==
-	*[[Alanine racemase\|Alanine racemase]]	+	*[[Alanine racemase 3D structures\|Alanine racemase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 41:		Line 41:
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Hu, T]]		[[Category: Hu, T]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]

OCA at 07:53, 31 October 2018

OCA — Wed, 31 Oct 2018 07:53:02 GMT

←Older revision		Revision as of 07:53, 31 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of Escherichia coli alaine racemase mutant E221A==		==Crystal structure of Escherichia coli alaine racemase mutant E221A==
	<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://pdbe.org/3b8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u 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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://pdbe.org/3b8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b8/3b8u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b8/3b8u_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>

OCA at 16:41, 8 February 2016

OCA — Mon, 08 Feb 2016 16:41:05 GMT

←Older revision		Revision as of 16:41, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3b8u]] is a 4 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=3B8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B8U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3b8u]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B8U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([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">alr ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u 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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://pdbe.org/3b8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	<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=3b8u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	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 3b8u" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
-	[[Category: ~~Escherichia coli~~]]	+	[[Category: Ecoli]]
	[[Category: Hu, T]]		[[Category: Hu, T]]
	[[Category: Jiang, H]]		[[Category: Jiang, H]]

OCA at 00:44, 25 December 2014

OCA — Thu, 25 Dec 2014 00:44:15 GMT

←Older revision		Revision as of 00:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3b8u]] is a 4 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=3B8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B8U FirstGlance]. <br>		<table><tr><td colspan='2'>[[3b8u]] is a 4 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=3B8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B8U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([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">alr ([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/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u 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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI]] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 39:
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Hu, T.]]	+	[[Category: Hu, T]]
-	[[Category: Jiang, H.]]	+	[[Category: Jiang, H]]
-	[[Category: Shen, X.]]	+	[[Category: Shen, X]]
-	[[Category: Wu, D.]]	+	[[Category: Wu, D]]
-	[[Category: Zhang, L.]]	+	[[Category: Zhang, L]]
	[[Category: Alpha/beta barrel]]		[[Category: Alpha/beta barrel]]
	[[Category: Cell shape]]		[[Category: Cell shape]]

OCA at 21:08, 2 October 2014

OCA — Thu, 02 Oct 2014 21:08:23 GMT

←Older revision		Revision as of 21:08, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3b8u.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Escherichia coli alaine racemase mutant E221A==
		+	<StructureSection load='3b8u' size='340' side='right' caption='[[3b8u]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3b8u]] is a 4 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=3B8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B8U FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2rjg\|2rjg]], [[2rjh\|2rjh]], [[3b8t\|3b8t]], [[3b8v\|3b8v]], [[3b8w\|3b8w]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alr ([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/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [http://www.ebi.ac.uk/pdbsum/3b8u 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/b8/3b8u_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 ==
		+	Alanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L-alanine and D-alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D-cycloserine-bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D- to L-Ala and L- to D-Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr.

-	~~{{STRUCTURE_3b8u\| PDB=3b8u \| SCENE= }}~~	+	Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis.,Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X Protein Sci. 2008 Jun;17(6):1066-76. Epub 2008 Apr 23. PMID:18434499<ref>PMID:18434499</ref>

-	~~===Crystal structure~~ of ~~Escherichia coli alaine racemase mutant E221A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_18434499}}~~	+	==See Also==
-		+	*[[Alanine racemase\|Alanine racemase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3b8u~~]] is a 4 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=3B8U OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:018434499<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "3b8u" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:50:27 GMT

Protected "3b8u" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:50, 7 January 2013

OCA at 20:50, 7 January 2013

OCA — Mon, 07 Jan 2013 20:50:23 GMT

←Older revision		Revision as of 20:50, 7 January 2013
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-	{{Seed}}
	[[Image:3b8u.png\|left\|200px]]		[[Image:3b8u.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3b8u\| PDB=3b8u \| SCENE= }}		{{STRUCTURE_3b8u\| PDB=3b8u \| SCENE= }}

	===Crystal structure of Escherichia coli alaine racemase mutant E221A===		===Crystal structure of Escherichia coli alaine racemase mutant E221A===

-
-	<!--
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	{{ABSTRACT_PUBMED_18434499}}		{{ABSTRACT_PUBMED_18434499}}

	==About this Structure==		==About this Structure==
-	~~3B8U~~ is a 4 ~~chains~~ structure ~~of sequences~~ 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=3B8U OCA].	+	[[3b8u]] is a 4 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=3B8U OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18434499~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018434499</ref><references group="xtra"/>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 37:		Line 25:
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:31:31 2009''

OCA at 22:31, 16 February 2009

OCA — Mon, 16 Feb 2009 22:31:33 GMT

←Older revision		Revision as of 22:31, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3B8U is a ~~[[Single protein]]~~ 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=3B8U OCA].	+	3B8U is a 4 chains structure of sequences 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=3B8U OCA].

	==Reference==		==Reference==
-	Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis., Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X, Protein Sci. 2008 Jun;17(6):1066-76. Epub 2008 Apr 23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18434499 18434499]~~	+	<ref group="xtra">PMID:18434499</ref><references group="xtra"/>
	[[Category: Alanine racemase]]		[[Category: Alanine racemase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Hu, T.]]		[[Category: Hu, T.]]
	[[Category: Jiang, H.]]		[[Category: Jiang, H.]]
Line 39:		Line 38:
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 04~~:57:~~48 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:31:31 2009''

OCA at 01:57, 28 July 2008

OCA — Mon, 28 Jul 2008 01:57:51 GMT

←Older revision		Revision as of 01:57, 28 July 2008
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	{{Seed}}		{{Seed}}
-	[[Image:3b8u.~~jpg~~\|left\|200px]]	+	[[Image:3b8u.png\|left\|200px]]

	<!--		<!--
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	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Jul ~~9 10~~:31:22 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:57:48 2008''