2z7b

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[[Image:2z7b.jpg|left|200px]]<br /><applet load="2z7b" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2z7b, resolution 1.900&Aring;" />
 
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'''Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase'''<br />
 
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==Overview==
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==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
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The function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (HMPDdc), an enzyme involved in the catabolism of pyridoxal 5'-phosphate (Vitamin B6). This enzyme was overexpressed in Escherichia coli and characterized. HMPDdc is a 26 kDa protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. The KM and kcat were found to be 366 microM and 0.6 s-1, respectively. The structure of this enzyme was determined at 1.9 A resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.
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<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2z7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_japonicum_MAFF_303099 Mesorhizobium japonicum MAFF 303099]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7B FirstGlance]. <br>
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2Z7B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti] with <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/3-hydroxy-2-methylpyridine-4,5-dicarboxylate_4-decarboxylase 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.51 4.1.1.51] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z7B OCA].
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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]] 1.9&#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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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==Reference==
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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=2z7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7b OCA], [https://pdbe.org/2z7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7b RCSB], [https://www.ebi.ac.uk/pdbsum/2z7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7b ProSAT]</span></td></tr>
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Gene identification and structural characterization of the pyridoxal 5'-phosphate degradative protein 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase from mesorhizobium loti MAFF303099., Mukherjee T, McCulloch KM, Ealick SE, Begley TP, Biochemistry. 2007 Nov 27;46(47):13606-15. Epub 2007 Oct 31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17973403 17973403]
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</table>
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[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
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== Function ==
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[[Category: Mesorhizobium loti]]
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[https://www.uniprot.org/uniprot/HMPD_RHILO HMPD_RHILO] Involved in the catabolism of pyridoxal 5-phosphate (Vitamin B6). Catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to yield 3-hydroxy-2-methylpyridine-5-carboxylate. The decarboxylation proceeds by an aldolase-like mechanism in which the binding of the substrate frees Glu-73 residue from its interaction with manganese ion replacing it by an interaction with the hydroxyl group from the substrate. Glu-73 residue then provides the proton for the keto-enol tautomerization. The decarboxylation reaction is analogous to the retroaldol reaction except that it does not need a base as the carboxylate is likely to be deprotonated under the reaction conditions.<ref>PMID:17973403</ref>
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Begley, T P.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Ealick, S E.]]
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Check<jmol>
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[[Category: McCulloch, K M.]]
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<jmolCheckbox>
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[[Category: Mukherjee, T.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>
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[[Category: MN]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: class ii aldolase superfamily]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: lyase]]
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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=2z7b ConSurf].
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:00:40 2008''
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Mesorhizobium japonicum MAFF 303099]]
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[[Category: Begley TP]]
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[[Category: Ealick SE]]
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[[Category: McCulloch KM]]
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[[Category: Mukherjee T]]

Current revision

Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase

PDB ID 2z7b

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