3daa - Revision history

OCA at 06:47, 9 August 2023

2023-08-09T06:47:57Z

← Older revision		Revision as of 06:47, 9 August 2023
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	<StructureSection load='3daa' size='340' side='right'caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3daa' size='340' side='right'caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacym Bacym~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3DAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._YM-1 Bacillus sp. YM-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PDD:N~~-~~(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</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]] 1.9Å</td></tr>
	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/D~~-~~amino~~-~~acid_transaminase~~ D-~~amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21]~~ </~~span~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [~~http~~://pdbe.org/3daa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3daa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa 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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [https://pdbe.org/3daa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [https://www.ebi.ac.uk/pdbsum/3daa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM]] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</ref>		[https://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</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: ~~Bacym]]~~		[[Category: Bacillus sp. YM-1]]
	~~[[Category: D~~-~~amino-acid transaminase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chipman~~, D M~~]]		[[Category: Chipman DM]]
	[[Category: Peisach, D]]		[[Category: Peisach D]]
	[[Category: Ringe, D]]		[[Category: Ringe D]]
	~~[[Category: Aminotransferase]]~~
	~~[[Category: Pyridoxal phosphate]]~~
	~~[[Category: Transaminase~~]]

OCA at 06:57, 19 August 2020

2020-08-19T06:57:24Z

← Older revision		Revision as of 06:57, 19 August 2020
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	==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==		==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==
	<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3daa' size='340' side='right'caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacym Bacym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacym Bacym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://pdbe.org/3daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa 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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://pdbe.org/3daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
	*[[Aminotransferase\|Aminotransferase]]		*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	*[[Aspartate ~~Aminotransferase~~\|Aspartate ~~Aminotransferase~~]]		*[[Aspartate aminotransferase 3D structures\|Aspartate aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Bacym]]		[[Category: Bacym]]
	[[Category: D-amino-acid transaminase]]		[[Category: D-amino-acid transaminase]]
			[[Category: Large Structures]]
	[[Category: Chipman, D M]]		[[Category: Chipman, D M]]
	[[Category: Peisach, D]]		[[Category: Peisach, D]]

OCA at 09:29, 14 November 2018

2018-11-14T09:29:36Z

← Older revision		Revision as of 09:29, 14 November 2018
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	==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==		==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==
	<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://pdbe.org/3daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa 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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://pdbe.org/3daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3daa 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/da/3daa_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/3daa_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==
	*[[Aminotransferase\|Aminotransferase]]		*[[Aminotransferase\|Aminotransferase]]
			*[[Aspartate Aminotransferase\|Aspartate Aminotransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:45, 9 February 2016

2016-02-09T16:45:33Z

← Older revision		Revision as of 16:45, 9 February 2016
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	<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_sp. Bacillus sp.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacym Bacym]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa 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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://pdbe.org/3daa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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=3daa ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3daa" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Aminotransferase\|Aminotransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus sp~~]]		[[Category: Bacym]]
	[[Category: D-amino-acid transaminase]]		[[Category: D-amino-acid transaminase]]
	[[Category: Chipman, D M]]		[[Category: Chipman, D M]]

OCA at 08:09, 25 December 2014

2014-12-25T08:09:35Z

← Older revision		Revision as of 08:09, 25 December 2014
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	<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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa 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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DAAA_BACYM DAAA_BACYM]] Acts on the D-isomers of alanine, leucine, aspartate, glutamate, aminobutyrate, norvaline and asparagine. The enzyme transfers an amino group from a substrate D-amino acid to the pyridoxal phosphate cofactor to form pyridoxamine and an alpha-keto acid in the first half-reaction. The second-half reaction is the reverse of the first, transferring the amino group from the pyridoxamine to a second alpha-keto acid to form the product D-amino acid via a ping-pong mechanism. This is an important process in the formation of D-alanine and D-glutamate, which are essential bacterial cell wall components.<ref>PMID:2914916</ref> <ref>PMID:9538014</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:13, 12 November 2014

2014-11-12T08:13:04Z

← Older revision		Revision as of 08:13, 12 November 2014
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	[[Image:~~3daa~~.~~png~~\|~~left~~\|~~200px~~]]		==CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE==
			<StructureSection load='3daa' size='340' side='right' caption='[[3daa]], [[Resolution\|resolution]] 1.90Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DAA FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_transaminase D-amino-acid transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.21 2.6.1.21] </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=3daa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3daa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3daa RCSB], [http://www.ebi.ac.uk/pdbsum/3daa 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/da/3daa_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 three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.

	~~{{STRUCTURE_3daa\| PDB=3daa \| SCENE= }}~~		Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.,Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D Biochemistry. 1998 Apr 7;37(14):4958-67. PMID:9538014<ref>PMID:9538014</ref>

	~~===CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_9538014}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3daa]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_sp~~. ~~Bacillus sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA].~~		</StructureSection>
			[[Category: Bacillus sp]]
	==~~Reference~~==
	<~~ref group="xtra">PMID:009538014<~~/~~ref~~>~~<ref group="xtra">PMID:011264579~~</~~ref><references group="xtra"/~~>
	[[Category: Bacillus sp.]]
	[[Category: D-amino-acid transaminase]]		[[Category: D-amino-acid transaminase]]
	[[Category: Chipman, D M.]]		[[Category: Chipman, D M]]
	[[Category: Peisach, D.]]		[[Category: Peisach, D]]
	[[Category: Ringe, D.]]		[[Category: Ringe, D]]
	[[Category: Aminotransferase]]		[[Category: Aminotransferase]]
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
	[[Category: Transaminase]]		[[Category: Transaminase]]

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

2013-01-07T19:23:28Z

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

← Older revision	Revision as of 19:23, 7 January 2013
(No difference)

OCA at 19:23, 7 January 2013

2013-01-07T19:23:23Z

← Older revision		Revision as of 19:23, 7 January 2013
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	~~{{Seed}}~~
	[[Image:3daa.png\|left\|200px]]		[[Image:3daa.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3daa", 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_3daa\| PDB=3daa \| SCENE= }}		{{STRUCTURE_3daa\| PDB=3daa \| SCENE= }}

	===CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE===		===CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_9538014}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 9538014 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_9538014}}		{{ABSTRACT_PUBMED_9538014}}

	==About this Structure==		==About this Structure==
	~~3DAA~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA].		[[3daa]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~9538014~~</ref><references group="xtra"/>		<ref group="xtra">PMID:009538014</ref><ref group="xtra">PMID:011264579</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: D-amino-acid transaminase]]		[[Category: D-amino-acid transaminase]]
Line 32:		Line 20:
	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
	[[Category: Transaminase]]		[[Category: Transaminase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:17:04 2009''~~

OCA at 09:17, 17 February 2009

2009-02-17T09:17:05Z

← Older revision		Revision as of 09:17, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3DAA is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA].		3DAA is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DAA OCA].

	==Reference==		==Reference==
	~~Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase., Peisach D, Chipman DM, Van Ophem PW, Manning JM, Ringe D, Biochemistry. 1998 Apr 7;37(14):4958-67.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9538014 9538014]~~		<ref group="xtra">PMID:9538014</ref><references group="xtra"/>
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]
	[[Category: D-amino-acid transaminase]]		[[Category: D-amino-acid transaminase]]
	~~[[Category: Single protein]]~~
	[[Category: Chipman, D M.]]		[[Category: Chipman, D M.]]
	[[Category: Peisach, D.]]		[[Category: Peisach, D.]]
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	[[Category: Transaminase]]		[[Category: Transaminase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 15~~:20:~~29 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:17:04 2009''

OCA at 12:20, 28 July 2008

2008-07-28T12:20:36Z

← Older revision		Revision as of 12:20, 28 July 2008
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	[[Image:3daa.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:3daa.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3daa\| PDB=3daa \| SCENE= }}		{{STRUCTURE_3daa\| PDB=3daa \| SCENE= }}

	~~'''~~CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE~~'''~~		===CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE===


	~~==Overview==~~		<!--
	The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, ~~N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of~~ the ~~enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us~~ to ~~describe~~ the ~~pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues~~ (~~Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group~~. ~~The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity~~. ~~As in L-aspartate aminotransferase (L-AspAT~~), the ~~cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction~~. ~~Unlike L~~-~~AspAT, D~~-~~aAT shows no other significant conformational changes during the reaction.~~		The line below this paragraph, {{ABSTRACT_PUBMED_9538014}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 9538014 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_9538014}}

	==About this Structure==		==About this Structure==
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	[[Category: Pyridoxal phosphate]]		[[Category: Pyridoxal phosphate]]
	[[Category: Transaminase]]		[[Category: Transaminase]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:00:01 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:20:29 2008''