4q9d | pdb_00004q9d

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

spinqualitylabelsall models 4q9d, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4q9d is a 2 chain structure with sequence from Mycs2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: FMT, MG Gene: MSMEG_1606, MSMEI_1567 (MYCS2) Activity: Benzoylformate decarboxylase, with EC number 4.1.1.7 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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