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1mcz

From Proteopedia

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[[Image:1mcz.gif|left|200px]]
 
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{{Structure
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==BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE==
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|PDB= 1mcz |SIZE=350|CAPTION= <scene name='initialview01'>1mcz</scene>, resolution 2.8&Aring;
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<StructureSection load='1mcz' size='340' side='right'caption='[[1mcz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RMN:(R)-MANDELIC+ACID'>RMN</scene>, <scene name='pdbligand=TDP:THIAMIN+DIPHOSPHATE'>TDP</scene>
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<table><tr><td colspan='2'>[[1mcz]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MCZ FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoylformate_decarboxylase Benzoylformate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.7 4.1.1.7] </span>
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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]] 2.8&#8491;</td></tr>
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|GENE= MDLC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RMN:(R)-MANDELIC+ACID'>RMN</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
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|DOMAIN=
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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=1mcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mcz OCA], [https://pdbe.org/1mcz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mcz RCSB], [https://www.ebi.ac.uk/pdbsum/1mcz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mcz ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1bfd|1BFD]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mcz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mcz OCA], [http://www.ebi.ac.uk/pdbsum/1mcz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1mcz RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/MDLC_PSEPU MDLC_PSEPU]
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== Evolutionary Conservation ==
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'''BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mc/1mcz_consurf.spt"</scriptWhenChecked>
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Benzoylformate decarboxylase is a member of the family of enzymes that are dependent on the cofactor thiamin diphosphate. A structure of this enzyme binding (R)-mandelate, a competitive inhibitor, suggests that at least two hydrogen bonds are formed between the substrate, benzoylformate, and active site side chains. The first is between the carboxylate group of benzoylformate and the hydroxyl group of S26, and the second is between carbonyl group of the substrate and an imidazole nitrogen of H70. Steady-state kinetic studies indicate that the catalytic parameters are strongly affected in three active site mutants, S26A, H70A, and H281A. The K(m) of S26A was increased most dramatically, 25-fold more than that of the wild-type enzyme, while the K(i) of (R)-mandelate was increased 100-fold, suggesting that the serine hydroxyl is important for substrate binding. The k(cat) of H70A is reduced more than 3 orders of magnitude, strongly implicating this residue in catalysis, and H281 showed significant, but smaller magnitude, effects on both K(m) and k(cat). Stopped-flow experiments using an alternative substrate, p-nitrobenzoylformate, lead to kinetic resolution of the fate of key thiamin diphosphate-bound intermediates. Together, the experimental results suggest the following roles for residues in the active site. The residue H70 is important for the protonation of the 2-alpha-mandelyl-ThDP intermediate, thereby assisting in decarboxylation, and for the deprotonation of the 2-alpha-hydroxybenzyl-ThDP intermediate, aiding product release. H281 is involved in protonation of the enamine. Surprisingly, S26 appears to be involved not only in substrate binding but also in other steps of the reaction.
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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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==About this Structure==
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</jmolCheckbox>
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1MCZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCZ OCA].
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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=1mcz ConSurf].
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<div style="clear:both"></div>
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==Reference==
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__TOC__
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Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase., Polovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL, Hasson MS, Biochemistry. 2003 Feb 25;42(7):1820-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12590569 12590569]
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</StructureSection>
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[[Category: Benzoylformate decarboxylase]]
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[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Single protein]]
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[[Category: Bera AK]]
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[[Category: Bera, A K.]]
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[[Category: Hasson MS]]
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[[Category: Hasson, M S.]]
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[[Category: Polovnikova ES]]
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[[Category: Polovnikova, E S.]]
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[[Category: decarboxylase]]
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[[Category: r-mandelate]]
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[[Category: thiamin diphosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:14:32 2008''
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Current revision

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE

PDB ID 1mcz

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