4FP1

P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl) propionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode.

Nagar, M.Lietzan, A.D.St Maurice, M.Bearne, S.L.

(2014) Biochemistry 53: 1169-1178

  • DOI: 10.1021/bi401703h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg(2+)-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Because trifluorolactate is also a substrate of MR, we anticipated that replacing the phenyl rings of ...

    Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg(2+)-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Because trifluorolactate is also a substrate of MR, we anticipated that replacing the phenyl rings of the competitive, substrate-product analogue inhibitor benzilate (Ki = 0.7 mM) with trifluoromethyl groups might furnish an inhibitor. Surprisingly, the substrate-product analogue 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoate (TFHTP) was a potent competitive inhibitor [Ki = 27 ± 4 μM; cf. Km = 1.2 mM for both (R)-mandelate and (R)-trifluorolactate]. To understand the origins of this high binding affinity, we determined the X-ray crystal structure of the MR-TFHTP complex to 1.68 Å resolution. Rather than chelating the active site Mg(2+) with its glycolate moiety, like other ground state analogues, TFHTP exhibited a novel binding mode with the two trifluoromethyl groups closely packed against the 20s loop and the carboxylate bridging the two active site Brønsted acid-base catalysts Lys 166 and His 297. Recognizing that positioning a carboxylate between the Brønsted acid-base catalysts could yield an inhibitor, we showed that tartronate was a competitive inhibitor of MR (Ki = 1.8 ± 0.1 mM). The X-ray crystal structure of the MR-tartronate complex (1.80 Å resolution) revealed that the glycolate moiety of tartronate chelated the Mg(2+) and that the carboxylate bridged Lys 166 and His 297. Models of tartronate in monomers A and B of the crystal structure mimicked the binding orientations of (S)-mandelate and that anticipated for (R)-mandelate, respectively. For the latter monomer, the 20s loop appeared to be disordered, as it also did in the X-ray structure of the MR triple mutant (C92S/C264S/K166C) complexed with benzilate, which was determined to 1.89 Å resolution. These observations indicate that the 20s loop likely undergoes a significant conformational change upon binding (R)-mandelate. In general, our observations suggest that inhibitors of other enolase superfamily enzymes may be designed to capitalize on the recognition of the active site Brønsted acid-base catalysts as binding determinants.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Dalhousie University , Halifax, Nova Scotia B3H 4R2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mandelate racemase
A, B
383Pseudomonas putidaMutation(s): 0 
Gene Names: mdlA
EC: 5.1.2.2
Find proteins for P11444 (Pseudomonas putida)
Go to UniProtKB:  P11444
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BFM
Query on BFM

Download SDF File 
Download CCD File 
A, B
3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoic acid
C4 H2 F6 O3
CMQUGOHGJUTDGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BFMKi: 27000 nM BINDINGMOAD
BFMKi: 27000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.169 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 148.870α = 90.00
b = 148.870β = 90.00
c = 169.640γ = 90.00
Software Package:
Software NamePurpose
MD2data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Database references
  • Version 1.2: 2014-03-12
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary
  • Version 1.4: 2018-01-31
    Type: Structure summary