3FSJ

Crystal structure of benzoylformate decarboxylase in complex with the inhibitor MBP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.

Brandt, G.S.Kneen, M.M.Chakraborty, S.Baykal, A.T.Nemeria, N.Yep, A.Ruby, D.I.Petsko, G.A.Kenyon, G.L.McLeish, M.J.Jordan, F.Ringe, D.

(2009) Biochemistry 48: 3247-3257

  • DOI: 10.1021/bi801950k
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control ...

    Benzoylformate decarboxylase (BFDC) is a thiamin diphosphate- (ThDP-) dependent enzyme acting on aromatic substrates. In addition to its metabolic role in the mandelate pathway, BFDC shows broad substrate specificity coupled with tight stereo control in the carbon-carbon bond-forming reverse reaction, making it a useful biocatalyst for the production of chiral alpha-hydroxy ketones. The reaction of methyl benzoylphosphonate (MBP), an analogue of the natural substrate benzoylformate, with BFDC results in the formation of a stable analogue (C2alpha-phosphonomandelyl-ThDP) of the covalent ThDP-substrate adduct C2alpha-mandelyl-ThDP. Formation of the stable adduct is confirmed both by formation of a circular dichroism band characteristic of the 1',4'-iminopyrimidine tautomeric form of ThDP (commonly observed when ThDP forms tetrahedral complexes with its substrates) and by high-resolution mass spectrometry of the reaction mixture. In addition, the structure of BFDC with the MBP inhibitor was solved by X-ray crystallography to a spatial resolution of 1.37 A (PDB ID 3FSJ). The electron density clearly shows formation of a tetrahedral adduct between the C2 atom of ThDP and the carbonyl carbon atom of the MBP. This adduct resembles the intermediate from the penultimate step of the carboligation reaction between benzaldehyde and acetaldehyde. The combination of real-time kinetic information via stopped-flow circular dichroism with steady-state data from equilibrium circular dichroism measurements and X-ray crystallography reveals details of the first step of the reaction catalyzed by BFDC. The MBP-ThDP adduct on BFDC is compared to the recently solved structure of the same adduct on benzaldehyde lyase, another ThDP-dependent enzyme capable of catalyzing aldehyde condensation with high stereospecificity.


    Organizational Affiliation

    Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Benzoylformate decarboxylaseX528Pseudomonas putidaMutation(s): 0 
Gene Names: mdlC
EC: 4.1.1.7
Find proteins for P20906 (Pseudomonas putida)
Explore P20906 
Go to UniProtKB:  P20906
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D7K
Query on D7K

Download CCD File 
X
3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
C20 H28 N4 O11 P3 S
NEEQBMRCDKRNBV-FQEVSTJZSA-O
 Ligand Interaction
CA
Query on CA

Download CCD File 
X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D7KKd:  5490000   nM  Binding MOAD
D7KKd :  113000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.484α = 90
b = 95.354β = 90
c = 137.139γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance