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

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

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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, F.H.Horton, J.D.Shin, D.Yoon, H.J.Logsdon, M.G.Malik, A.M.Rogers, M.P.Kneen, M.M.Suh, S.W.McLeish, M.J.

(2015) Biochim Biophys Acta 1854: 1001-1009

  • DOI: https://doi.org/10.1016/j.bbapap.2015.04.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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 2.2Å. 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 K(m) value for benzoylformate was ~23 mM, nearly 100-fold greater than that of PpBFDC while the k(cat) 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.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA. Electronic address: mcleish@iupui.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Benzoylformate decarboxylase
A, B
545Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1606MSMEI_1567
Find proteins for A0QSU7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QSU7 
Go to UniProtKB:  A0QSU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QSU7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.162α = 90
b = 137.162β = 90
c = 337.057γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references