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| | <StructureSection load='2z9v' size='340' side='right'caption='[[2z9v]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='2z9v' size='340' side='right'caption='[[2z9v]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2z9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700743 Atcc 700743]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2z9v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9V 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=PXM:4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL'>PXM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z9u|2z9u]], [[2z9w|2z9w]], [[2z9x|2z9x]]</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=PXM:4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL'>PXM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mlr6806 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=381 ATCC 700743])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyridoxamine--pyruvate_transaminase Pyridoxamine--pyruvate transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.30 2.6.1.30] </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=2z9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9v OCA], [https://pdbe.org/2z9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9v RCSB], [https://www.ebi.ac.uk/pdbsum/2z9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9v 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=2z9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9v OCA], [https://pdbe.org/2z9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9v RCSB], [https://www.ebi.ac.uk/pdbsum/2z9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9v ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PPAT_RHILO PPAT_RHILO] Catalyzes a reversible transamination reaction between pyridoxamine and pyruvate to form pyridoxal and L-alanine.<ref>PMID:16545075</ref> <ref>PMID:17989071</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 700743]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyridoxamine--pyruvate transaminase]] | + | [[Category: Mesorhizobium loti]] |
| - | [[Category: Hayashi, H]] | + | [[Category: Hayashi H]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Mizutani, K]] | + | [[Category: Mizutani K]] |
| - | [[Category: Ohnishi, K]] | + | [[Category: Ohnishi K]] |
| - | [[Category: Yagi, T]] | + | [[Category: Yagi T]] |
| - | [[Category: Yamasaki, M]] | + | [[Category: Yamasaki M]] |
| - | [[Category: Yokochi, N]] | + | [[Category: Yokochi N]] |
| - | [[Category: Yoshikane, Y]] | + | [[Category: Yoshikane Y]] |
| - | [[Category: Aminotransferase]]
| + | |
| - | [[Category: Pyridoxamine]]
| + | |
| - | [[Category: Pyruvate]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PPAT_RHILO Catalyzes a reversible transamination reaction between pyridoxamine and pyruvate to form pyridoxal and L-alanine.[1] [2]
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
Pyridoxamine-pyruvate aminotransferase (PPAT; EC 2.6.1.30) is a pyridoxal 5'-phosphate-independent aminotransferase and catalyzes reversible transamination between pyridoxamine and pyruvate to form pyridoxal and L-alanine. The crystal structure of PPAT from Mesorhizobium loti has been solved in space group P4(3)2(1)2 and was refined to an R factor of 15.6% (R(free) = 20.6%) at 2.0 A resolution. In addition, the structures of PPAT in complexes with pyridoxamine, pyridoxal, and pyridoxyl-L-alanine have been refined to R factors of 15.6, 15.4, and 14.5% (R(free) = 18.6, 18.1, and 18.4%) at 1.7, 1.7, and 2.0 A resolution, respectively. PPAT is a homotetramer and each subunit is composed of a large N-terminal domain, consisting of seven beta-sheets and eight alpha-helices, and a smaller C-terminal domain, consisting of three beta-sheets and four alpha-helices. The substrate pyridoxal is bound through an aldimine linkage to Lys-197 in the active site. The alpha-carboxylate group of the substrate amino/keto acid is hydrogen-bonded to Arg-336 and Arg-345. The structures revealed that the bulky side chain of Glu-68 interfered with the binding of the phosphate moiety of pyridoxal 5'-phosphate and made PPAT specific to pyridoxal. The reaction mechanism of the enzyme is discussed based on the structures and kinetics results.
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.,Yoshikane Y, Yokochi N, Yamasaki M, Mizutani K, Ohnishi K, Mikami B, Hayashi H, Yagi T J Biol Chem. 2008 Jan 11;283(2):1120-7. Epub 2007 Nov 6. PMID:17989071[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Yoshikane Y, Yokochi N, Ohnishi K, Hayashi H, Yagi T. Molecular cloning, expression and characterization of pyridoxamine-pyruvate aminotransferase. Biochem J. 2006 Jun 15;396(3):499-507. PMID:16545075 doi:10.1042/BJ20060078
- ↑ Yoshikane Y, Yokochi N, Yamasaki M, Mizutani K, Ohnishi K, Mikami B, Hayashi H, Yagi T. Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099. J Biol Chem. 2008 Jan 11;283(2):1120-7. Epub 2007 Nov 6. PMID:17989071 doi:http://dx.doi.org/10.1074/jbc.M708061200
- ↑ Yoshikane Y, Yokochi N, Yamasaki M, Mizutani K, Ohnishi K, Mikami B, Hayashi H, Yagi T. Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099. J Biol Chem. 2008 Jan 11;283(2):1120-7. Epub 2007 Nov 6. PMID:17989071 doi:http://dx.doi.org/10.1074/jbc.M708061200
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