1MDL

MANDELATE RACEMASE MUTANT K166R CO-CRYSTALLIZED WITH (R)-MANDELATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant.

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

(1995) Biochemistry 34: 2788-2797


  • PubMed Abstract: 
  • On the basis of the available high-resolution structures of mandelate racemase (MR) from Pseudomonas putida [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) Bio ...

    On the basis of the available high-resolution structures of mandelate racemase (MR) from Pseudomonas putida [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], Lys 166 and His 297 are positioned appropriately to participate in catalysis as acid/base catalysts that either abstract the alpha-proton from the enantiomers of mandelate to form an enolic intermediate or protonate the enolic intermediate to form the enantiomers of mandelate, with Lys 166 participating as the (S)-specific acid/base catalyst and His 297 participating as the (R)-specific acid/base catalyst. In this paper we report the structural and mechanistic properties of the mutant in which Lys 166 has been replaced with arginine (K166R). The structure of K166R has been determined at 1.85 A resolution with the substrate (S)-mandelate bound in the active site. The structure of this complex reveals no geometric alterations in the active site, with the exception that the longer side chain of Arg 166 is necessarily displaced upward from the position occupied by Lys 166 by steric interactions with the bound substrate. In contrast to the H297N mutant of MR [Landro, J. A., Kallarakal, A. T., Ransom, S. C., Gerlt, J. A., Kozarich, J. W., Neidhart, D. J., & Kenyon, G. L. (1991) Biochemistry 30, 9275-9281], the K166R exhibits low levels of racemase activity [kcat is reduced 5 x 10(3)-fold in the (R)- to (S)-direction and 1 x 10(3)-fold in the (S)- to (R)-direction]. The substrate and solvent deuterium isotope effects support a reaction coordinate for the K166R-catalyzed reaction in which the transition state for interconversion of bound (S)-mandelate and the stabilized enolic intermediate is higher in energy that the transition state for interconversion of bound (R)-mandelate and the stabilized enolic intermediate. The solvent deuterium isotope effect when (S)-mandelate is substrate (2.2 +/- 0.3) supports the proposal that the formation of the enolic intermediate involves partial transfer of a solvent-derived proton from Glu 317 to the substrate as the alpha-proton is abstracted [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].(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANDELATE RACEMASE
A
359Pseudomonas putidaMutation(s): 1 
Gene Names: mdlA
EC: 5.1.2.2
Find proteins for P11444 (Pseudomonas putida)
Go to UniProtKB:  P11444
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RMN
Query on RMN

Download SDF File 
Download CCD File 
A
(R)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-SSDOTTSWSA-N
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
A
(S)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-ZETCQYMHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RMNKi: 590000 - 810000 nM (99) BINDINGDB
SMNKi: 570000 nM (99) BINDINGDB
RMNKi: 810000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.184 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.320α = 90.00
b = 125.320β = 90.00
c = 106.420γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other
  • Version 1.4: 2018-03-14
    Type: Database references