1DTN

MANDELATE RACEMASE MUTANT D270N CO-CRYSTALLIZED WITH (S)-ATROLACTATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317.

Mitra, B.Kallarakal, A.T.Kozarich, J.W.Gerlt, J.A.Clifton, J.G.Petsko, G.A.Kenyon, G.L.

(1995) Biochemistry 34: 2777-2787

  • DOI: 10.1021/bi00009a006
  • Primary Citation of Related Structures:  
    1DTN

  • PubMed Abstract: 
  • In the high-resolution X-ray structure of mandelate racemase (MR) with the competitive inhibitor (S)-atrolactate bound in the active site [Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., & Petsko, G ...

    In the high-resolution X-ray structure of mandelate racemase (MR) with the competitive inhibitor (S)-atrolactate bound in the active site [Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, J., & Petsko, G. A. (1994) Biochemistry 33, 635-643], the carboxylic acid group of Glu 317 is hydrogen-bonded to the carboxylate group of the bound inhibitor. This geometry suggests that the carboxylic acid functional group of Glu 317 participates as a general acid catalyst in the concerted general acid-general base catalyzed formation of a stabilized enolic tautomer of mandelic acid as a reaction intermediate. To test this hypothesis, the E317Q mutant of MR was constructed and subjected to high-resolution X-ray structural analysis in the presence of (S)-atrolactate. No conformational alterations were observed to accompany the E317Q substitution at 2.1 A resolution. The values for kcat were reduced 4.5 x 10(3)-fold for (R)-mandelate and 2.9 x 10(4)-fold for (S)-mandelate; the values for kcat/Km were reduced 3 x 10(4)-fold. The substrate and solvent deuterium isotope effects measured for both wild-type MR and the E317Q mutant are not multiplicative when deuteriated substrate is studied in D2O, which suggests that the reactions catalyzed by both enzymes are stepwise and involve the formation of stabilized enolic intermediates. In contrast to wild-type MR, E317Q does not catalyze detectable elimination of bromide ion from either enantiomer of p-(bromomethyl)mandelate. However, E317Q is irreversibly inactivated by racemic alpha-phenylglycidate at a rate comparable to that measured for wild-type MR. Taken together, these mechanistic properties confirm the importance of Glu 317 as a general acid catalyst in the reaction catalyzed by wild-type MR. The kcat for wild-type MR and the reduction in kcat observed for E317O are discussed in terms of the analysis recently described by Gerlt and Gassman for understanding the rates and mechanisms of enzyme-catalyzed proton abstraction reactions from carbon acids [Gerlt, J. A., & Gassman, P. G. (1993) J. Am. Chem. Soc. 115, 11552-11568; Gerlt, J. A., & Gassman, P. G. (1993) Biochemistry 32, 11943-11952].


    Related Citations: 
    • Mechanism of the Reaction Catalyzed by Mandelate Racemase. 2. Crystal Structure of Mandelate Racemase at 2.5-A Resolution: Identification of the Active Site and Possible Catalytic Residues
      Neidhart, D.J., Howell, P.L., Petsko, G.A., Powers, V.M., Li, R.S., Kenyon, G.L., Gerlt, J.A.
      (1991) Biochemistry 30: 9264
    • Mandelate Racemase and Muconate Lactonizing Enzyme are Mechanistically Distinct and Structurally Homologous
      Neidhart, D.J., Kenyon, G.L., Gerlt, J.A., Petsko, G.A.
      (1990) Nature 347: 692

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland, College Park 20742.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANDELATE RACEMASEA359Pseudomonas aeruginosaMutation(s): 1 
Gene Names: MANDELATE RACEMASE
EC: 5.1.2.2
UniProt
Find proteins for P11444 (Pseudomonas putida)
Explore P11444 
Go to UniProtKB:  P11444
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APG (Subject of Investigation/LOI)
Query on APG

Download Ideal Coordinates CCD File 
C [auth A]ATROLACTIC ACID (2-PHENYL-LACTIC ACID)
C9 H10 O3
NWCHELUCVWSRRS-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.171 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.5α = 90
b = 125.5β = 90
c = 107.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance