4q9d

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==X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from Mycobacterium smegmatis==
==X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from Mycobacterium smegmatis==
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<StructureSection load='4q9d' size='340' side='right' caption='[[4q9d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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<StructureSection load='4q9d' size='340' side='right'caption='[[4q9d]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4q9d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q9D FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4q9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q9D 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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.2&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4q9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q9d OCA], [http://pdbe.org/4q9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q9d RCSB], [http://www.ebi.ac.uk/pdbsum/4q9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q9d ProSAT]</span></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=4q9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q9d OCA], [https://pdbe.org/4q9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q9d RCSB], [https://www.ebi.ac.uk/pdbsum/4q9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q9d ProSAT]</span></td></tr>
</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/A0QSU7_MYCS2 A0QSU7_MYCS2]
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Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate. It is the penultimate enzyme in both the mandelate pathway and the d-phenylglycine degradation pathway. The ThDP-dependent Enzyme Engineering Database (TEED) now lists more than 800 sequences annotated as BFDCs, including one from Mycobacterium smegmatis (MsBFDC). However, there is no evidence that either pathway for benzoylformate formation exists in the M. smegmatis genome. Further, sequence alignments of MsBFDC with the well characterized enzyme isolated from Pseudomonas putida (PpBFDC) indicate that there will be active site substitutions in MsBFDC likely to reduce activity with benzoylformate. Taken together these data would suggest that the annotation is unlikely to be correct. To test this hypothesis the putative MsBFDC was cloned, expressed, purified, and the X-ray structure was solved to a resolution of 2.2A. While showing no evidence for ThDP in the active site, the structure was very similar to that of PpBFDC. A number of 2-oxo acids were tested as substrates. For MsBFDC the Km value for benzoylformate was ~23mM, nearly 100-fold greater than that of PpBFDC while the kcat value was reduced 60-fold. These values would suggest that benzoylformate is not the physiological substrate for this enzyme, and that annotation as a 2-oxo acid decarboxylase may be more appropriate.
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The kinetic characterization and X-ray structure of a putative benzoylformate decarboxylase from M. smegmatis highlights the difficulties in the functional annotation of ThDP-dependent enzymes.,Andrews FH, Horton JD, Shin D, Yoon HJ, Logsdon MG, Malik AM, Rogers MP, Kneen MM, Suh SW, McLeish MJ Biochim Biophys Acta. 2015 Apr 30;1854(8):1001-1009. doi:, 10.1016/j.bbapap.2015.04.027. PMID:25936776<ref>PMID:25936776</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 4q9d" 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: Benzoylformate decarboxylase]]
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[[Category: Large Structures]]
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[[Category: Andrews, F H]]
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[[Category: Mycolicibacterium smegmatis MC2 155]]
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[[Category: Horton, J D]]
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[[Category: Andrews FH]]
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[[Category: Kneen, M M]]
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[[Category: Horton JD]]
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[[Category: Logsdon, M G]]
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[[Category: Kneen MM]]
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[[Category: Malik, A M.K]]
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[[Category: Logsdon MG]]
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[[Category: McLeish, M J]]
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[[Category: Malik AMK]]
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[[Category: Shin, D H]]
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[[Category: McLeish MJ]]
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[[Category: Suh, S W]]
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[[Category: Shin DH]]
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[[Category: Yoon, H J]]
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[[Category: Suh SW]]
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[[Category: Lyase]]
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[[Category: Yoon HJ]]
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[[Category: Thiamin diphosphate-dependent decarboxylase]]
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Current revision

X-ray structure of a putative thiamin diphosphate-dependent enzyme isolated from Mycobacterium smegmatis

PDB ID 4q9d

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