2z7b: Difference between revisions

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[[Image:2z7b.jpg|left|200px]]


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==Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase==
The line below this paragraph, containing "STRUCTURE_2z7b", creates the "Structure Box" on the page.
<StructureSection load='2z7b' size='340' side='right'caption='[[2z7b]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_2z7b|  PDB=2z7b  |  SCENE= }}
<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>
 
</table>
'''Crystal Structure of Mesorhizobium loti 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase'''
== Function ==
 
[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>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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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==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7b_consurf.spt"</scriptWhenChecked>
2Z7B is a [[Single protein]] structure of sequence 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=2Z7B OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/17973403 17973403]
</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].
[[Category: 3-hydroxy-2-methylpyridine-4,5-dicarboxylate 4-decarboxylase]]
<div style="clear:both"></div>
[[Category: Mesorhizobium loti]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Begley, T P.]]
__TOC__
[[Category: Ealick, S E.]]
</StructureSection>
[[Category: McCulloch, K M.]]
[[Category: Large Structures]]
[[Category: Mukherjee, T.]]
[[Category: Mesorhizobium japonicum MAFF 303099]]
[[Category: Class ii aldolase superfamily]]
[[Category: Begley TP]]
[[Category: Lyase]]
[[Category: Ealick SE]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:01:26 2008''
[[Category: McCulloch KM]]
[[Category: Mukherjee T]]
Retrieved from "https://proteopedia.org/2z7b"