1m7j - Revision history

OCA at 13:26, 13 March 2024

OCA — Wed, 13 Mar 2024 13:26:51 GMT

←Older revision		Revision as of 13:26, 13 March 2024
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	<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Alcfa Alcfa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.5Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [https://pdbe.org/1m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [https://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j 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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [https://pdbe.org/1m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [https://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9AGH8_ALCFA Q9AGH8_ALCFA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1m7j 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=1m7j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino acids. We report here the first D-aminoacylase crystal structure from A. faecalis at 1.5-A resolution. The protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion. The enzyme structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well. Unexpectedly, the enzyme binds two zinc ions with widely different affinities, although only the tightly bound zinc ion is required for activity. One zinc ion is coordinated by Cys(96), His(220), and His(250), while the other is loosely chelated by His(67), His(69), and Cys(96). This is the first example of the metal ion coordination by a cysteine residue in the superfamily. Therefore, D-aminoacylase defines a novel subset and is a mononuclear zinc metalloenzyme but containing a binuclear active site. The preferred substrate was modeled into a hydrophobic pocket, revealing the substrate specificity and enzyme catalysis. The 63-residue insertion containing substrate-interacting residues may act as a gate controlling access to the active site, revealing that the substrate binding would induce a closed conformation to sequester the catalysis from solvent.
-
-	Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism.,Liaw SH, Chen SJ, Ko TP, Hsu CS, Chen CJ, Wang AH, Tsai YC J Biol Chem. 2003 Feb 14;278(7):4957-62. Epub 2002 Nov 25. PMID:12454005<ref>PMID:12454005</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aminoacylase 3D structures\|Aminoacylase 3D structures]]		*[[Aminoacylase 3D structures\|Aminoacylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcfa~~]]	+	[[Category: Alcaligenes faecalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: N-acyl-D-amino-acid deacylase]]~~	+	[[Category: Chen S-J]]
-	[[Category: Chen, S J]]	+	[[Category: Hsu C-S]]
-	[[Category: Hsu, C S]]	+	[[Category: Ko T-P]]
-	[[Category: Ko, T P]]	+	[[Category: Liaw S-H]]
-	[[Category: Liaw, S H]]	+	[[Category: Tsai Y-C]]
-	[[Category: Tsai, Y C]]	+	[[Category: Wang AH-J]]
-	[[Category: Wang~~, A H.~~J]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal-dependent amidohydrolase]]~~	+
-	~~[[Category: Tin-barrel~~]]	+

OCA at 08:54, 21 April 2021

OCA — Wed, 21 Apr 2021 08:54:07 GMT

←Older revision		Revision as of 08:54, 21 April 2021
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	<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [~~http~~://pdbe.org/1m7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j 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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [https://pdbe.org/1m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [https://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 12:57, 17 July 2019

OCA — Wed, 17 Jul 2019 12:57:29 GMT

←Older revision		Revision as of 12:57, 17 July 2019
Line 1:		Line 1:

	==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==		==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==
-	<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m7/1m7j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m7/1m7j_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 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1m7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m7j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminoacylase 3D structures\|Aminoacylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Alcfa]]		[[Category: Alcfa]]
		+	[[Category: Large Structures]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]
	[[Category: Chen, S J]]		[[Category: Chen, S J]]

OCA at 10:16, 12 October 2017

OCA — Thu, 12 Oct 2017 10:16:23 GMT

←Older revision		Revision as of 10:16, 12 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==		==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==
	<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://pdbe.org/1m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j 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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://pdbe.org/1m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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=1m7j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1m7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m7j" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[D-aminoacylase\|D-aminoacylase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:09, 11 September 2015

OCA — Fri, 11 Sep 2015 11:09:38 GMT

←Older revision		Revision as of 11:09, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Alcaligenes_faecalis Alcaligenes faecalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j 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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://pdbe.org/1m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1m7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcaligenes faecalis~~]]	+	[[Category: Alcfa]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]
	[[Category: Chen, S J]]		[[Category: Chen, S J]]

OCA at 16:19, 5 January 2015

OCA — Mon, 05 Jan 2015 16:19:57 GMT

←Older revision		Revision as of 16:19, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j 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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]
-	[[Category: Chen, S J.]]	+	[[Category: Chen, S J]]
-	[[Category: Hsu, C S.]]	+	[[Category: Hsu, C S]]
-	[[Category: Ko, T P.]]	+	[[Category: Ko, T P]]
-	[[Category: Liaw, S H.]]	+	[[Category: Liaw, S H]]
-	[[Category: Tsai, Y C.]]	+	[[Category: Tsai, Y C]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Wang, A H.J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metal-dependent amidohydrolase]]		[[Category: Metal-dependent amidohydrolase]]
	[[Category: Tin-barrel]]		[[Category: Tin-barrel]]

OCA at 13:36, 28 September 2014

OCA — Sun, 28 Sep 2014 13:36:56 GMT

←Older revision		Revision as of 13:36, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1m7j.~~png\|left~~\|200px]]	+	==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==
		+	<StructureSection load='1m7j' size='340' side='right' caption='[[1m7j]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] </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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [http://www.ebi.ac.uk/pdbsum/1m7j 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/m7/1m7j_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 ==
		+	D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino acids. We report here the first D-aminoacylase crystal structure from A. faecalis at 1.5-A resolution. The protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion. The enzyme structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well. Unexpectedly, the enzyme binds two zinc ions with widely different affinities, although only the tightly bound zinc ion is required for activity. One zinc ion is coordinated by Cys(96), His(220), and His(250), while the other is loosely chelated by His(67), His(69), and Cys(96). This is the first example of the metal ion coordination by a cysteine residue in the superfamily. Therefore, D-aminoacylase defines a novel subset and is a mononuclear zinc metalloenzyme but containing a binuclear active site. The preferred substrate was modeled into a hydrophobic pocket, revealing the substrate specificity and enzyme catalysis. The 63-residue insertion containing substrate-interacting residues may act as a gate controlling access to the active site, revealing that the substrate binding would induce a closed conformation to sequester the catalysis from solvent.

-	~~{{STRUCTURE_1m7j\| PDB=1m7j \| SCENE= }}~~	+	Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism.,Liaw SH, Chen SJ, Ko TP, Hsu CS, Chen CJ, Wang AH, Tsai YC J Biol Chem. 2003 Feb 14;278(7):4957-62. Epub 2002 Nov 25. PMID:12454005<ref>PMID:12454005</ref>

-	~~===Crystal structure of D-aminoacylase defines~~ a ~~novel subset~~ of ~~amidohydrolases===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12454005}}~~	+	==See Also==
-		+	*[[D-aminoacylase\|D-aminoacylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1m7j~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012454005<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]

OCA: Protected "1m7j" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:33:57 GMT

Protected "1m7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:33, 5 December 2012

OCA at 20:33, 5 December 2012

OCA — Wed, 05 Dec 2012 20:33:52 GMT

←Older revision		Revision as of 20:33, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1m7j.png\|left\|200px]]		[[Image:1m7j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1m7j", 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_1m7j\| PDB=1m7j \| SCENE= }}		{{STRUCTURE_1m7j\| PDB=1m7j \| SCENE= }}

	===Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases===		===Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12454005}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12454005 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12454005}}		{{ABSTRACT_PUBMED_12454005}}

	==About this Structure==		==About this Structure==
-	~~1M7J~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].	+	[[1m7j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12454005~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012454005</ref><references group="xtra"/>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]
Line 32:		Line 20:
	[[Category: Tsai, Y C.]]		[[Category: Tsai, Y C.]]
	[[Category: Wang, A H.J.]]		[[Category: Wang, A H.J.]]
		+	[[Category: Hydrolase]]
	[[Category: Metal-dependent amidohydrolase]]		[[Category: Metal-dependent amidohydrolase]]
	[[Category: Tin-barrel]]		[[Category: Tin-barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:40:12 2009''

OCA at 18:40, 17 February 2009

OCA — Tue, 17 Feb 2009 18:40:13 GMT

←Older revision		Revision as of 18:40, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1M7J is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].	+	1M7J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].

	==Reference==		==Reference==
-	Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism., Liaw SH, Chen SJ, Ko TP, Hsu CS, Chen CJ, Wang AH, Tsai YC, J Biol Chem. 2003 Feb 14;278(7):4957-62. Epub 2002 Nov 25. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12454005 12454005]~~	+	<ref group="xtra">PMID:12454005</ref><references group="xtra"/>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: N-acyl-D-amino-acid deacylase]]		[[Category: N-acyl-D-amino-acid deacylase]]
-	[[Category: Single protein]]
	[[Category: Chen, S J.]]		[[Category: Chen, S J.]]
	[[Category: Hsu, C S.]]		[[Category: Hsu, C S.]]
Line 36:		Line 35:
	[[Category: Tin-barrel]]		[[Category: Tin-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 23~~:23:~~01 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:40:12 2009''