1MCZ

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH AN INHIBITOR, R-MANDELATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase

POLOVNIKOVA, E.S.McLeish, M.J.Sergienko, E.A.Burgner, J.T.Anderson, N.L.BERA, A.K.Jordan, F.Kenyon, G.L.HASSON, M.S.

(2003) Biochemistry 42: 1820-1830

  • DOI: 10.1021/bi026490k
  • Primary Citation of Related Structures:  
    1MCZ

  • PubMed Abstract: 
  • Benzoylformate decarboxylase is a member of the family of enzymes that are dependent on the cofactor thiamin diphosphate. A structure of this enzyme binding (R)-mandelate, a competitive inhibitor, suggests that at least two hydrogen bonds are formed between the substrate, benzoylformate, and active site side chains ...

    Benzoylformate decarboxylase is a member of the family of enzymes that are dependent on the cofactor thiamin diphosphate. A structure of this enzyme binding (R)-mandelate, a competitive inhibitor, suggests that at least two hydrogen bonds are formed between the substrate, benzoylformate, and active site side chains. The first is between the carboxylate group of benzoylformate and the hydroxyl group of S26, and the second is between carbonyl group of the substrate and an imidazole nitrogen of H70. Steady-state kinetic studies indicate that the catalytic parameters are strongly affected in three active site mutants, S26A, H70A, and H281A. The K(m) of S26A was increased most dramatically, 25-fold more than that of the wild-type enzyme, while the K(i) of (R)-mandelate was increased 100-fold, suggesting that the serine hydroxyl is important for substrate binding. The k(cat) of H70A is reduced more than 3 orders of magnitude, strongly implicating this residue in catalysis, and H281 showed significant, but smaller magnitude, effects on both K(m) and k(cat). Stopped-flow experiments using an alternative substrate, p-nitrobenzoylformate, lead to kinetic resolution of the fate of key thiamin diphosphate-bound intermediates. Together, the experimental results suggest the following roles for residues in the active site. The residue H70 is important for the protonation of the 2-alpha-mandelyl-ThDP intermediate, thereby assisting in decarboxylation, and for the deprotonation of the 2-alpha-hydroxybenzyl-ThDP intermediate, aiding product release. H281 is involved in protonation of the enamine. Surprisingly, S26 appears to be involved not only in substrate binding but also in other steps of the reaction.


    Related Citations: 
    • The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes
      Hasson, M.S., Muscate, A., McLeish, M.J., Polovnikova, L.S., Gerlt, J.A., Kenyon, G.L., Petsko, G.A., Ringe, D.
      (1998) Biochemistry 37: 9918

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BENZOYLFORMATE DECARBOXYLASEABCDEFGHABCDEFGHIJKLMNOP
528Pseudomonas 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TDP
Query on TDP

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
THIAMIN DIPHOSPHATE
C12 H18 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-N
 Ligand Interaction
RMN
Query on RMN

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
(R)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-SSDOTTSWSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RMNKi :  1000000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.8α = 90
b = 209.6β = 97.1
c = 163.4γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance