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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/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"><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">[[3fa4|3fa4]]</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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</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='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://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> |
| | + | == 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]] |
| | 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> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2,3-dimethylmalate lyase]] | + | [[Category: Aspergillus niger]] |
| - | [[Category: A. niger]] | + | [[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]]
| + | |
| Structural highlights
Function
Q2L887_ASPNG
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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 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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O. Structure and Function of 2,3-Dimethylmalate Lyase, a PEP Mutase/Isocitrate Lyase Superfamily Member. J Mol Biol. 2008 Dec 24. PMID:19133276 doi:S0022-2836(08)01549-0
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