2hbv - Revision history

OCA at 09:31, 14 February 2024

OCA — Wed, 14 Feb 2024 09:31:53 GMT

←Older revision		Revision as of 09:31, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='2hbv' size='340' side='right'caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2hbv' size='340' side='right'caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus~~ fluorescens ~~liquefaciens" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=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]] 1.65Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2hbx\|2hbx]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>nbaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~294~~ "~~Bacillus fluorescens liquefaciens~~" ~~Flugge 1886])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </~~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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [https://pdbe.org/2hbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [https://www.ebi.ac.uk/pdbsum/2hbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbv 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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [https://pdbe.org/2hbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [https://www.ebi.ac.uk/pdbsum/2hbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q83V25_PSEFL Q83V25_PSEFL]
	== 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=2hbv 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=2hbv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) is a widespread enzyme found in many bacterial species and all currently sequenced eukaryotic organisms. It occupies a key position at the branching point of two metabolic pathways: the tryptophan to quinolinate pathway and the bacterial 2-nitrobenzoic acid degradation pathway. The activity of ACMSD determines whether the metabolites in both pathways are converted to quinolinic acid for NAD biosynthesis or to acetyl-CoA for the citric acid cycle. Here we report the first high-resolution crystal structure of ACMSD from Pseudomonas fluorescens which validates our previous predictions that this enzyme is a member of the metal-dependent amidohydrolase superfamily of the (beta/alpha)(8) TIM barrel fold. The structure of the enzyme in its native form, determined at 1.65 A resolution, reveals the precise spatial arrangement of the active site metal center and identifies a potential substrate-binding pocket. The identity of the native active site metal was determined to be Zn. Also determined was the structure of the enzyme complexed with cobalt at 2.50 A resolution. The hydrogen bonding network around the metal center suggests that Arg51 and His228 may play important roles in catalysis. The metal center configuration of PfACMSD is very similar to that of Zn-dependent adenosine deaminase and Fe-dependent cytosine deaminase, suggesting that ACMSD may share certain similarities in its catalytic mechanism with these enzymes. These data enable us to propose possible catalytic mechanisms for ACMSD which appear to be unprecedented among all currently characterized decarboxylases.
-
-	Crystal structure of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylation reaction.,Martynowski D, Eyobo Y, Li T, Yang K, Liu A, Zhang H Biochemistry. 2006 Sep 5;45(35):10412-21. PMID:16939194<ref>PMID:16939194</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2hbv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
-	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Eyobo, Y]]	+	[[Category: Pseudomonas fluorescens]]
-	[[Category: Li, T]]	+	[[Category: Eyobo Y]]
-	[[Category: Liu, A]]	+	[[Category: Li T]]
-	[[Category: Martynowski, D]]	+	[[Category: Liu A]]
-	[[Category: Yang, K]]	+	[[Category: Martynowski D]]
-	[[Category: Zhang, H]]	+	[[Category: Yang K]]
-	~~[[Category: Acmsd]]~~	+	[[Category: Zhang H]]
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metaloenzyme]]~~	+
-	~~[[Category: Tim-barrel~~]]	+

OCA at 07:36, 17 March 2021

OCA — Wed, 17 Mar 2021 07:36:13 GMT

←Older revision		Revision as of 07:36, 17 March 2021
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	==Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)==		==Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)==
-	<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='2hbv' size='340' side='right'caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2HBV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HBV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hbx\|2hbx]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [~~http~~://pdbe.org/2hbv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2hbv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbv 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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [https://pdbe.org/2hbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [https://www.ebi.ac.uk/pdbsum/2hbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hb/2hbv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hb/2hbv_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 35:		Line 35:
	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]		[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
		+	[[Category: Large Structures]]
	[[Category: Eyobo, Y]]		[[Category: Eyobo, Y]]
	[[Category: Li, T]]		[[Category: Li, T]]

OCA at 08:10, 18 October 2017

OCA — Wed, 18 Oct 2017 08:10:00 GMT

←Older revision		Revision as of 08:10, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)==		==Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)==
	<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://pdbe.org/2hbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv 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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://pdbe.org/2hbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hbv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 05:20, 9 February 2016

OCA — Tue, 09 Feb 2016 05:20:41 GMT

←Older revision		Revision as of 05:20, 9 February 2016
Line 17:		Line 17:
	<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=2hbv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:01, 10 September 2015

OCA — Thu, 10 Sep 2015 19:01:16 GMT

←Older revision		Revision as of 19:01, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_fluorescens Pseudomonas~~ fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_liquefaciens"_flugge_1886 "bacillus fluorescens liquefaciens" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 ~~Pseudomonas~~ fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 "Bacillus fluorescens liquefaciens" Flugge 1886])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv 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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://pdbe.org/2hbv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 2hbv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens liquefaciens flugge 1886]]
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
-	[[Category: Pseudomonas fluorescens]]
	[[Category: Eyobo, Y]]		[[Category: Eyobo, Y]]
	[[Category: Li, T]]		[[Category: Li, T]]

OCA at 09:32, 16 January 2015

OCA — Fri, 16 Jan 2015 09:32:14 GMT

←Older revision		Revision as of 09:32, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBV FirstGlance]. <br>		<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv 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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv 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 33:		Line 33:
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Eyobo, Y.]]	+	[[Category: Eyobo, Y]]
-	[[Category: Li, T.]]	+	[[Category: Li, T]]
-	[[Category: Liu, A.]]	+	[[Category: Liu, A]]
-	[[Category: Martynowski, D.]]	+	[[Category: Martynowski, D]]
-	[[Category: Yang, K.]]	+	[[Category: Yang, K]]
-	[[Category: Zhang, H.]]	+	[[Category: Zhang, H]]
	[[Category: Acmsd]]		[[Category: Acmsd]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]

OCA at 10:58, 30 September 2014

OCA — Tue, 30 Sep 2014 10:58:25 GMT

←Older revision		Revision as of 10:58, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2hbv.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)==
		+	<StructureSection load='2hbv' size='340' side='right' caption='[[2hbv]], [[Resolution\|resolution]] 1.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HBV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2hbx\|2hbx]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=294 Pseudomonas fluorescens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminocarboxymuconate-semialdehyde_decarboxylase Aminocarboxymuconate-semialdehyde decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.45 4.1.1.45] </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=2hbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hbv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2hbv RCSB], [http://www.ebi.ac.uk/pdbsum/2hbv 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/hb/2hbv_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 ==
		+	Alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD) is a widespread enzyme found in many bacterial species and all currently sequenced eukaryotic organisms. It occupies a key position at the branching point of two metabolic pathways: the tryptophan to quinolinate pathway and the bacterial 2-nitrobenzoic acid degradation pathway. The activity of ACMSD determines whether the metabolites in both pathways are converted to quinolinic acid for NAD biosynthesis or to acetyl-CoA for the citric acid cycle. Here we report the first high-resolution crystal structure of ACMSD from Pseudomonas fluorescens which validates our previous predictions that this enzyme is a member of the metal-dependent amidohydrolase superfamily of the (beta/alpha)(8) TIM barrel fold. The structure of the enzyme in its native form, determined at 1.65 A resolution, reveals the precise spatial arrangement of the active site metal center and identifies a potential substrate-binding pocket. The identity of the native active site metal was determined to be Zn. Also determined was the structure of the enzyme complexed with cobalt at 2.50 A resolution. The hydrogen bonding network around the metal center suggests that Arg51 and His228 may play important roles in catalysis. The metal center configuration of PfACMSD is very similar to that of Zn-dependent adenosine deaminase and Fe-dependent cytosine deaminase, suggesting that ACMSD may share certain similarities in its catalytic mechanism with these enzymes. These data enable us to propose possible catalytic mechanisms for ACMSD which appear to be unprecedented among all currently characterized decarboxylases.

-	~~{{STRUCTURE_2hbv\| PDB=2hbv \| SCENE= }}~~	+	Crystal structure of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylation reaction.,Martynowski D, Eyobo Y, Li T, Yang K, Liu A, Zhang H Biochemistry. 2006 Sep 5;45(35):10412-21. PMID:16939194<ref>PMID:16939194</ref>

-	~~===Crystal Structure~~ of ~~alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16939194}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2hbv]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016939194<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]

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

OCA — Mon, 07 Jan 2013 12:44:50 GMT

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

←Older revision

Revision as of 12:44, 7 January 2013

OCA at 12:44, 7 January 2013

OCA — Mon, 07 Jan 2013 12:44:48 GMT

←Older revision		Revision as of 12:44, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2hbv.png\|left\|200px]]		[[Image:2hbv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2hbv", 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_2hbv\| PDB=2hbv \| SCENE= }}		{{STRUCTURE_2hbv\| PDB=2hbv \| SCENE= }}

	===Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)===		===Crystal Structure of alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde-Decarboxylase (ACMSD)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16939194}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16939194 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16939194}}		{{ABSTRACT_PUBMED_16939194}}

	==About this Structure==		==About this Structure==
-	~~2HBV~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA].	+	[[2hbv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fluorescens Pseudomonas fluorescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HBV OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16939194~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016939194</ref><references group="xtra"/>
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
Line 34:		Line 22:
	[[Category: Acmsd]]		[[Category: Acmsd]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]
		+	[[Category: Lyase]]
	[[Category: Metaloenzyme]]		[[Category: Metaloenzyme]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:47:29 2009''

OCA at 04:47, 17 February 2009

OCA — Tue, 17 Feb 2009 04:47:31 GMT

←Older revision		Revision as of 04:47, 17 February 2009
Line 20:		Line 20:

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

	==Reference==		==Reference==
-	Crystal structure of alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylation reaction., Martynowski D, Eyobo Y, Li T, Yang K, Liu A, Zhang H, Biochemistry. 2006 Sep 5;45(35):10412-21. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16939194 16939194]~~	+	<ref group="xtra">PMID:16939194</ref><references group="xtra"/>
	[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]		[[Category: Aminocarboxymuconate-semialdehyde decarboxylase]]
	[[Category: Pseudomonas fluorescens]]		[[Category: Pseudomonas fluorescens]]
-	[[Category: Single protein]]
	[[Category: Eyobo, Y.]]		[[Category: Eyobo, Y.]]
	[[Category: Li, T.]]		[[Category: Li, T.]]
Line 38:		Line 37:
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 10~~:24:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:47:29 2009''