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 

Starting Model: experimental
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This is version 2.1 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: https://doi.org/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. 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BENZOYLFORMATE DECARBOXYLASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
528Pseudomonas putidaMutation(s): 0 
Gene Names: MDLC
EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida)
Explore P20906 
Go to UniProtKB:  P20906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20906
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth D]
EB [auth L]
GA [auth E]
HB [auth M]
AB [auth K],
CA [auth D],
EB [auth L],
GA [auth E],
HB [auth M],
JA [auth F],
LB [auth N],
MA [auth G],
OB [auth O],
QA [auth H],
S [auth A],
SB [auth P],
UA [auth I],
V [auth B],
XA [auth J],
Y [auth C]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
RMN
Query on RMN

Download Ideal Coordinates CCD File 
BB [auth K]
DA [auth D]
FB [auth L]
HA [auth E]
IB [auth M]
BB [auth K],
DA [auth D],
FB [auth L],
HA [auth E],
IB [auth M],
KA [auth F],
MB [auth N],
NA [auth G],
PB [auth O],
RA [auth H],
T [auth A],
TB [auth P],
VA [auth I],
W [auth B],
YA [auth J],
Z [auth C]
(R)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-SSDOTTSWSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CB [auth L]
DB [auth L]
EA [auth E]
AA [auth D],
BA [auth D],
CB [auth L],
DB [auth L],
EA [auth E],
FA [auth E],
GB [auth M],
IA [auth F],
JB [auth N],
KB [auth N],
LA [auth G],
NB [auth O],
OA [auth H],
PA [auth H],
Q [auth A],
QB [auth P],
R [auth A],
RB [auth P],
SA [auth I],
TA [auth I],
U [auth B],
WA [auth J],
X [auth C],
ZA [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RMN PDBBind:  1MCZ Ki: 1.00e+6 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-14
    Changes: Data collection, Database references, Refinement description