3fa3 - Revision history

OCA at 00:29, 28 December 2023

2023-12-28T00:29:58Z

← Older revision		Revision as of 00:29, 28 December 2023
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	<StructureSection load='3fa3' size='340' side='right'caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3fa3' size='340' side='right'caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/~~A._niger A.~~ niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:~~2~~,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</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]] 2.6Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3fa4\|3fa4]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>
	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b></td><td class="sblockDat">An07g08390~~ (~~[https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger]~~)~~</td~~></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/~~2,~~3-dimethylmalate_lyase~~ 2,3-~~dimethylmalate lyase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=4.1.~~3~~.32 4.1.~~3~~.32]~~ </~~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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [https://pdbe.org/3fa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fa3 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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [https://pdbe.org/3fa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fa3 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q2L887_ASPNG Q2L887_ASPNG]
	== 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: ~~2,3-dimethylmalate lyase]]~~		[[Category: Aspergillus niger]]
	~~[[Category: A.~~ niger]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Herzberg, O]]		[[Category: Herzberg O]]
	[[Category: Narayanan~~, B C]]~~		[[Category: Narayanan BC]]
	~~[[Category: Alpha/beta barrel]]~~
	~~[[Category: Helix swapping]]~~
	~~[[Category: Lyase~~]]

OCA at 09:27, 23 February 2022

2022-02-23T09:27:21Z

← Older revision		Revision as of 09:27, 23 February 2022
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	==Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form==		==Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form==
	<StructureSection load='3fa3' size='340' side='right' caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3fa3' size='340' side='right'caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fa4\|3fa4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3fa4\|3fa4]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">An07g08390 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">An07g08390 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/2,3-dimethylmalate_lyase 2,3-dimethylmalate lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.32 4.1.3.32] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2,3-dimethylmalate_lyase 2,3-dimethylmalate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.32 4.1.3.32] </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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [~~http~~://pdbe.org/3fa3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3fa3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3fa3 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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [https://pdbe.org/3fa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [https://www.ebi.ac.uk/pdbsum/3fa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fa3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: A. niger]]		[[Category: A. niger]]
			[[Category: Large Structures]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Narayanan, B C]]		[[Category: Narayanan, B C]]

OCA at 07:46, 5 December 2018

2018-12-05T07:46:30Z

← Older revision		Revision as of 07:46, 5 December 2018
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/fa/3fa3_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/3fa3_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 15:29, 11 August 2016

2016-08-11T15:29:52Z

← Older revision		Revision as of 15:29, 11 August 2016
Line 1:		Line 1:

	==Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form==		==Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form==
	<StructureSection load='3fa3' size='340' side='right' caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3fa3' size='340' side='right' caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aspergillus_niger Aspergillus~~ niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fa4\|3fa4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fa4\|3fa4]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">An07g08390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 ~~Aspergillus~~ niger])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">An07g08390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3-dimethylmalate_lyase 2,3-dimethylmalate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.32 4.1.3.32] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3-dimethylmalate_lyase 2,3-dimethylmalate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.32 4.1.3.32] </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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [http://www.ebi.ac.uk/pdbsum/3fa3 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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [http://pdbe.org/3fa3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [http://www.ebi.ac.uk/pdbsum/3fa3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fa3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<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=3fa3 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 3fa3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: ~~Aspergillus~~ niger]]		[[Category: A. niger]]
	[[Category: Herzberg, O]]		[[Category: Herzberg, O]]
	[[Category: Narayanan, B C]]		[[Category: Narayanan, B C]]

OCA at 08:36, 26 November 2014

2014-11-26T08:36:30Z

← Older revision		Revision as of 08:36, 26 November 2014
Line 1:		Line 1:
	[[Image:~~3fa3~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form==
			<StructureSection load='3fa3' size='340' side='right' caption='[[3fa3]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3fa3]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FA3 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OAF:2,2-DIFLUORO-3,3-DIHYDROXYBUTANEDIOIC+ACID'>OAF</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3fa4\|3fa4]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">An07g08390 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 Aspergillus niger])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3-dimethylmalate_lyase 2,3-dimethylmalate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.32 4.1.3.32] </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=3fa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fa3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3fa3 RCSB], [http://www.ebi.ac.uk/pdbsum/3fa3 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/fa/3fa3_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 Aspergillus niger genome contains four genes that encode proteins exhibiting greater than 30% amino acid sequence identity to the confirmed oxaloacetate acetyl hydrolase (OAH), an enzyme that belongs to the phosphoenolpyruvate mutase/isocitrate lyase superfamily. Previous studies have shown that a mutant A. niger strain lacking the OAH gene does not produce oxalate. To identify the function of the protein sharing the highest amino acid sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the protein in Escherichia coli and purified it for structural and functional studies. A focused substrate screen was used to determine the catalytic function of An07g08390 as (2R,3S)-dimethylmalate lyase (DMML): k(cat)=19.2 s(-1) and K(m)=220 muM. DMML also possesses significant OAH activity (k(cat)=0.5 s(-1) and K(m) =220 muM). DNA array analysis showed that unlike the A. niger oah gene, the DMML encoding gene is subject to catabolite repression. DMML is a key enzyme in bacterial nicotinate catabolism, catalyzing the last of nine enzymatic steps. This pathway does not have a known fungal counterpart. BLAST analysis of the A. niger genome for the presence of a similar pathway revealed the presence of homologs to only some of the pathway enzymes. This and the finding that A. niger does not thrive on nicotinamide as a sole carbon source suggest that the fungal DMML functions in a presently unknown metabolic pathway. The crystal structure of A. niger DMML (in complex with Mg(2+) and in complex with Mg(2+) and a substrate analog: the gem-diol of 3,3-difluoro-oxaloacetate) was determined for the purpose of identifying structural determinants of substrate recognition and catalysis. Structure-guided site-directed mutants were prepared and evaluated to test the contributions made by key active-site residues. In this article, we report the results in the broader context of the lyase branch of the phosphoenolpyruvate mutase/isocitrate lyase superfamily to provide insight into the evolution of functional diversity.

	~~{{STRUCTURE_3fa3\| PDB=3fa3 \| SCENE= }}~~		Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member.,Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O J Mol Biol. 2008 Dec 24. PMID:19133276<ref>PMID:19133276</ref>

	~~===Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase~~/~~isocitrate lyase superfamily member~~, ~~trigonal crystal form===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19133276}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[3fa3]] is~~ a ~~16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aspergillus_niger Aspergillus niger]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:019133276<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: Aspergillus niger]]		[[Category: Aspergillus niger]]
	[[Category: Herzberg, O.]]		[[Category: Herzberg, O]]
	[[Category: Narayanan, B C.]]		[[Category: Narayanan, B C]]
	[[Category: Alpha/beta barrel]]		[[Category: Alpha/beta barrel]]
	[[Category: Helix swapping]]		[[Category: Helix swapping]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA: Protected "3fa3" [edit=sysop:move=sysop]

2013-02-13T10:54:03Z

Protected "3fa3" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:54, 13 February 2013
(No difference)

OCA at 10:54, 13 February 2013

2013-02-13T10:54:00Z

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	~~{{Seed}}~~
	[[Image:3fa3.png\|left\|200px]]		[[Image:3fa3.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3fa3", creates the "Structure Box" on the page.~~
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	{{STRUCTURE_3fa3\| PDB=3fa3 \| SCENE= }}		{{STRUCTURE_3fa3\| PDB=3fa3 \| SCENE= }}

	===Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form===		===Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19133276}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19133276 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19133276}}		{{ABSTRACT_PUBMED_19133276}}

	==About this Structure==		==About this Structure==
	~~3FA3~~ is a 16 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].		[[3fa3]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19133276~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019133276</ref><references group="xtra"/>
	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: Aspergillus niger]]		[[Category: Aspergillus niger]]
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	[[Category: Helix swapping]]		[[Category: Helix swapping]]
	[[Category: Lyase]]		[[Category: Lyase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:48:07 2010''~~

OCA at 08:39, 22 September 2010

2010-09-22T08:39:08Z

← Older revision		Revision as of 08:39, 22 September 2010
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	==About this Structure==		==About this Structure==
	3FA3 is a ~~[[Single protein]]~~ structure ~~of sequence~~ from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].		3FA3 is a 16 chains structure with sequences from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].

	==Reference==		==Reference==
	Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member., Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O, J Mol Biol. 2008 Dec 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19133276 19133276]~~		<ref group="xtra">PMID:19133276</ref><references group="xtra"/>
	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: Aspergillus niger]]		[[Category: Aspergillus niger]]
	[[Category: ~~Single protein~~]]		[[Category: Herzberg, O.]]
	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]		[[Category: Narayanan, B C.]]
	[[Category: Alpha/beta barrel]]		[[Category: Alpha/beta barrel]]
	[[Category: Helix swapping]]		[[Category: Helix swapping]]
	[[Category: Lyase]]		[[Category: Lyase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 20~~:13:~~30 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:48:07 2010''

OCA at 18:13, 4 March 2009

2009-03-04T18:13:31Z

← Older revision		Revision as of 18:13, 4 March 2009
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	==About this Structure==		==About this Structure==
	3FA3 is a ~~16 chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].		3FA3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FA3 OCA].

	==Reference==		==Reference==
	~~<ref group="xtra">~~PMID:~~19133276<~~/~~ref><references group="xtra"~~/>		Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member., Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O, J Mol Biol. 2008 Dec 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19133276 19133276]
	[[Category: 2,3-dimethylmalate lyase]]		[[Category: 2,3-dimethylmalate lyase]]
	[[Category: Aspergillus niger]]		[[Category: Aspergillus niger]]
	[[Category: ~~Herzberg, O.~~]]		[[Category: Single protein]]
	[[Category: ~~Narayanan~~, ~~B C~~.]]		[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
	[[Category: Alpha/beta barrel]]		[[Category: Alpha/beta barrel]]
	[[Category: Helix swapping]]		[[Category: Helix swapping]]
	[[Category: Lyase]]		[[Category: Lyase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:08:13 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 20:13:30 2009''

OCA at 12:08, 4 March 2009

2009-03-04T12:08:14Z

← Older revision		Revision as of 12:08, 4 March 2009
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	{{Seed}}		{{Seed}}
	[[Image:3fa3.~~jpg~~\|left\|200px]]		[[Image:3fa3.png\|left\|200px]]

	<!--		<!--
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	[[Category: Lyase]]		[[Category: Lyase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 28 09~~:50:59 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:08:13 2009''