4MQ5

Crystal Structure of Benzoylformate Decarboxylase Mutant A306F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.502 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Perturbation of the monomer-monomer interfaces of the benzoylformate decarboxylase tetramer.

Andrews, F.H.Rogers, M.P.Paul, L.N.McLeish, M.J.

(2014) Biochemistry 53: 4358-4367

  • DOI: 10.1021/bi500081r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray structure of benzoylformate decarboxylase (BFDC) from Pseudomonas putida ATCC 12633 shows it to be a tetramer. This was believed to be typical of all thiamin diphosphate-dependent decarboxylases until recently when the structure of KdcA, a ...

    The X-ray structure of benzoylformate decarboxylase (BFDC) from Pseudomonas putida ATCC 12633 shows it to be a tetramer. This was believed to be typical of all thiamin diphosphate-dependent decarboxylases until recently when the structure of KdcA, a branched-chain 2-keto acid decarboxylase from Lactococcus lactis, showed it to be a homodimer. This lent credence to earlier unfolding experiments on pyruvate decarboxylase from Saccharomyces cerevisiae that indicated that it might be active as a dimer. To investigate this possibility in BFDC, we sought to shift the equilibrium toward dimer formation. Point mutations were made in the noncatalytic monomer-monomer interfaces, but these had a minimal effect on both tetramer formation and catalytic activity. Subsequently, the R141E/Y288A/A306F variant was shown by analytical ultracentrifugation to be partially dimeric. It was also found to be catalytically inactive. Further experiments revealed that just two mutations, R141E and A306F, were sufficient to markedly alter the dimer-tetramer equilibrium and to provide an ~450-fold decrease in kcat. Equilibrium denaturation studies suggested that the residual activity was possibly due to the presence of residual tetramer. The structures of the R141E and A306F variants, determined to <1.5 Å resolution, hinted that disruption of the monomer interfaces will be accompanied by movement of a loop containing Leu109 and Leu110. As these residues contribute to the hydrophobicity of the active site and the correct positioning of the substrate, it seems that tetramer formation may well be critical to the catalytic activity of BFDC.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , Indianapolis, Indiana 46202, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Benzoylformate decarboxylase
A
536Pseudomonas putidaMutation(s): 1 
Gene Names: mdlC
EC: 4.1.1.7
Find proteins for P20906 (Pseudomonas putida)
Go to UniProtKB:  P20906
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

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Download CCD File 
A
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.502 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.120 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.629α = 90.00
b = 95.540β = 90.00
c = 137.590γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
Blu-Icedata collection
PHENIXmodel building
PHENIXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release