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New page: left|200px<br /><applet load="2z7b" size="350" color="white" frame="true" align="right" spinBox="true" caption="2z7b, resolution 1.900Å" /> '''Crystal Structure o...
 
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[[Image:2z7b.jpg|left|200px]]<br /><applet load="2z7b" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2z7b, resolution 1.900&Aring;" />
'''Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase'''<br />


==Overview==
==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
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 muM 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.
<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
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].
</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>
 
<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>
==Reference==
<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>
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 Oct 31;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17973403 17973403]
</table>
[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
== Function ==
[[Category: Mesorhizobium loti]]
[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>
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Begley, T.P.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Ealick, S.E.]]
Check<jmol>
[[Category: McCulloch, K.M.]]
  <jmolCheckbox>
[[Category: Mukherjee, T.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>
[[Category: MN]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: class ii aldolase superfamily]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: lyase]]
  </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=2z7b ConSurf].
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:50:32 2008''
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mesorhizobium japonicum MAFF 303099]]
[[Category: Begley TP]]
[[Category: Ealick SE]]
[[Category: McCulloch KM]]
[[Category: Mukherjee T]]

Latest revision as of 13:56, 13 March 2024

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

2z7b, resolution 1.90Å

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