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4gp9

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==Crystal Structure of Benzoylformate Decarboxylase Mutant L403F==
==Crystal Structure of Benzoylformate Decarboxylase Mutant L403F==
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<StructureSection load='4gp9' size='340' side='right' caption='[[4gp9]], [[Resolution|resolution]] 1.07&Aring;' scene=''>
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<StructureSection load='4gp9' size='340' side='right'caption='[[4gp9]], [[Resolution|resolution]] 1.07&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gp9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GP9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GP9 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gp9]] is a 1 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=4GP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GP9 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TZD:2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TZD</scene></td></tr>
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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]] 1.07&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gg1|4gg1]], [[4gm0|4gm0]], [[4gm1|4gm1]], [[4gm4|4gm4]], [[4gpe|4gpe]]</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TZD:2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TZD</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdlC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
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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=4gp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gp9 OCA], [https://pdbe.org/4gp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gp9 RCSB], [https://www.ebi.ac.uk/pdbsum/4gp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gp9 ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gp9 OCA], [http://pdbe.org/4gp9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gp9 RCSB], [http://www.ebi.ac.uk/pdbsum/4gp9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gp9 ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/MDLC_PSEPU MDLC_PSEPU]
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It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of a bulky hydrophobic residue located directly below the cofactor. Here we report the use of site-saturation mutagenesis to generate variants of this residue (Leu403) in benzoylformate decarboxylase. The observed 3 orders of magnitude range in kcat/Km values suggested that conformational changes in the cofactor could be influencing catalysis. However, X-ray structures of several variants were determined, and there was remarkably little change in ThDP conformation. Rather, it seemed that, once the V-conformation was attained, residue size and hydrophobicity were more important for enzyme activity.
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A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.,Andrews FH, Tom AR, Gunderman PR, Novak WR, McLeish MJ Biochemistry. 2013 May 7;52(18):3028-30. doi: 10.1021/bi400368j. Epub 2013 Apr, 23. PMID:23607689<ref>PMID:23607689</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4gp9" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus fluorescens putidus flugge 1886]]
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[[Category: Large Structures]]
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[[Category: Benzoylformate decarboxylase]]
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[[Category: Pseudomonas putida]]
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[[Category: Andrews, F H]]
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[[Category: Andrews FH]]
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[[Category: Gunderman, P R]]
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[[Category: Gunderman PR]]
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[[Category: McLeish, M J]]
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[[Category: McLeish MJ]]
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[[Category: Novak, W R.P]]
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[[Category: Novak WRP]]
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[[Category: Tom, A R]]
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[[Category: Tom AR]]
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[[Category: Decarboxylase]]
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[[Category: Lyase]]
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[[Category: Thiamin thiazolone diphosphate cofactor]]
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Current revision

Crystal Structure of Benzoylformate Decarboxylase Mutant L403F

PDB ID 4gp9

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