1MNS

ON THE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE FROM PSEUDOMONAS PUTIDA: MECHANISTIC AND CRYSTALLOGRAPHIC EVIDENCE FOR STEREOSPECIFIC ALKYLATION BY (R)-ALPHA-PHENYLGLYCIDATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate.

Landro, J.A.Gerlt, J.A.Kozarich, J.W.Koo, C.W.Shah, V.J.Kenyon, G.L.Neidhart, D.J.Fujita, S.Petsko, G.A.

(1994) Biochemistry 33: 635-643

  • Primary Citation of Related Structures:  1MDR

  • PubMed Abstract: 
  • The mechanism of irreversible inactivation of mandelate racemase (MR) from Pseudomonas putida by alpha-phenylglycidate (alpha PGA) has been investigated stereochemically and crystallographically. The (R) and (S) enantiomers of alpha PGA were synthesi ...

    The mechanism of irreversible inactivation of mandelate racemase (MR) from Pseudomonas putida by alpha-phenylglycidate (alpha PGA) has been investigated stereochemically and crystallographically. The (R) and (S) enantiomers of alpha PGA were synthesized in high enantiomeric excess (81% ee and 83% ee, respectively) using Sharpless epoxidation chemistry. (R)-alpha PGA was determined to be a stereospecific and stoichiometric irreversible inactivator of MR. (S)-alpha PGA does not inactivate MR and appears to bind noncovalently to the active site of MR with less affinity than that of (R)-alpha PGA. The X-ray crystal structure (2.0-A resolution) of MR inactivated by (R)-alpha PGA revealed the presence of a covalent adduct formed by nucleophilic attack of the epsilon-amino group of Lys 166 on the distal carbon on the epoxide ring of (R)-alpha PGA. The proximity of the alpha-proton of (S)-mandelate to Lys 166 [configurationally equivalent to (R)-alpha PGA] was corroborated by the crystal structure (2.1-A resolution) of MR complexed with the substrate analog/competitive inhibitor, (S)-atrolactate [(S)-alpha-methylmandelate]. These results support the proposal that Lys 166 is the polyvalent acid/base responsible for proton transfers on the (S) face of mandelate. In addition, the high-resolution structures also provide insight into the probable interactions of mandelate with the essential Mg2+ and functional groups in the active site.


    Related Citations: 
    • Mechanism of the Reaction Catalyzed by Mandelate Racemase 2. Crystal Structure of Mandelate Racemase at 2.5 Angstroms Resolution: Identification of the Active Site and Possible Catalytic Residues
      Neidhart, D.J.,Howell, P.L.,Petsko, G.A.,Powers, V.M.,Li, R.,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
    • Refined High-Resolution X-Ray Structures of Mandelate Racemase in Complex with Catalytically Active Metal Ions
      Neidhart, D.J.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANDELATE RACEMASE
A
357Pseudomonas putidaGene 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
APG
Query on APG

Download SDF File 
Download CCD File 
A
ATROLACTIC ACID (2-PHENYL-LACTIC ACID)
C9 H10 O3
NWCHELUCVWSRRS-VIFPVBQESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
APGKi: 67000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.153 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.000α = 90.00
b = 125.000β = 90.00
c = 105.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance