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2z9v

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{{Seed}}
 
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[[Image:2z9v.png|left|200px]]
 
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<!--
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==Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine==
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The line below this paragraph, containing "STRUCTURE_2z9v", creates the "Structure Box" on the page.
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<StructureSection load='2z9v' size='340' side='right'caption='[[2z9v]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<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>
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{{STRUCTURE_2z9v| PDB=2z9v | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z9/2z9v_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2z9v ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine===
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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<ref>PMID:17989071</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2z9v" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17989071}}, adds the Publication Abstract to the page
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*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17989071 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17989071}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2Z9V is a 2 chains structure of sequences from [http://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].
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==Reference==
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<ref group="xtra">PMID:17989071</ref><references group="xtra"/>
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[[Category: Mesorhizobium loti]]
[[Category: Mesorhizobium loti]]
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[[Category: Pyridoxamine--pyruvate transaminase]]
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[[Category: Hayashi H]]
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[[Category: Hayashi, H.]]
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[[Category: Mikami B]]
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[[Category: Mikami, B.]]
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[[Category: Mizutani K]]
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[[Category: Mizutani, K.]]
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[[Category: Ohnishi K]]
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[[Category: Ohnishi, K.]]
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[[Category: Yagi T]]
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[[Category: Yagi, T.]]
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[[Category: Yamasaki M]]
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[[Category: Yamasaki, M.]]
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[[Category: Yokochi N]]
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[[Category: Yokochi, N.]]
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[[Category: Yoshikane Y]]
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[[Category: Yoshikane, Y.]]
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[[Category: Aminotransferase]]
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[[Category: Pyridoxamine]]
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[[Category: Pyruvate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:13:27 2009''
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Current revision

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine

PDB ID 2z9v

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