2z9v: Difference between revisions
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== | ==Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine== | ||
<StructureSection load='2z9v' size='340' side='right'caption='[[2z9v]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<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='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='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='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> | |||
== 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 == | |||
[[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/z9/2z9v_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/main_output.php?pdb_ID=2z9v ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:17989071</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2z9v" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Aspartate aminotransferase 3D structures|Aspartate aminotransferase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mesorhizobium loti]] | [[Category: Mesorhizobium loti]] | ||
[[Category: Hayashi H]] | |||
[[Category: Mikami B]] | |||
[[Category: Hayashi | [[Category: Mizutani K]] | ||
[[Category: Mikami | [[Category: Ohnishi K]] | ||
[[Category: Mizutani | [[Category: Yagi T]] | ||
[[Category: Ohnishi | [[Category: Yamasaki M]] | ||
[[Category: Yagi | [[Category: Yokochi N]] | ||
[[Category: Yamasaki | [[Category: Yoshikane Y]] | ||
[[Category: Yokochi | |||
[[Category: Yoshikane | |||
