4JD5

Crystal Structure of Benzoylformate Decarboxylase Mutant L403E

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.

Andrews, F.H., Tom, A.R., Gunderman, P.R., Novak, W.R., McLeish, M.J.

(2013) Biochemistry 52: 3028-3030

  • DOI: 10.1021/bi400368j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of ...

    It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of a bulky hydrophobic residue located directly below the cofactor. Here we report the use of site-saturation mutagenesis to generate variants of this residue (Leu403) in benzoylformate decarboxylase. The observed 3 orders of magnitude range in k(cat)/K(m) values suggested that conformational changes in the cofactor could be influencing catalysis. However, X-ray structures of several variants were determined, and there was remarkably little change in ThDP conformation. Rather, it seemed that, once the V-conformation was attained, residue size and hydrophobicity were more important for enzyme activity.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA.




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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TZD
Query on TZD
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A
2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
THIAMIN THIAZOLONE DIPHOSPHATE
C12 H18 N4 O8 P2 S
ZGJUYGIRPQSCFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.134 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.550α = 90.00
b = 95.790β = 90.00
c = 137.150γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release