2OHV

Structural Basis for Glutamate Racemase Inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for glutamate racemase inhibition

Kim, K.H.Bong, Y.J.Park, J.K.Shin, K.J.Hwang, K.Y.Kim, E.E.

(2007) J.Mol.Biol. 372: 434-443

  • DOI: 10.1016/j.jmb.2007.05.003
  • Primary Citation of Related Structures:  2OHG, 2OHO

  • PubMed Abstract: 
  • D-Glutamic acid is a required biosynthetic building block for peptidoglycan, and the enzyme glutamate racemase (GluR) catalyzes the inter-conversion of D and L-glutamate enantiomers. Therefore, GluR is considered as an attractive target for the desig ...

    D-Glutamic acid is a required biosynthetic building block for peptidoglycan, and the enzyme glutamate racemase (GluR) catalyzes the inter-conversion of D and L-glutamate enantiomers. Therefore, GluR is considered as an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of GluR from Streptococcus pyogenes in both inhibitor-free and inhibitor-bound forms. The inhibitor free GluR crystallized in two different forms, which diffracted to 2.25 A and 2.5 A resolution, while the inhibitor-bound crystal diffracted to 2.5 A resolution. GluR is composed of two domains of alpha/beta protein that are related by pseudo-2-fold symmetry and the active site is located at the domain interface. The inhibitor, gamma-2-naphthylmethyl-D-glutamate, which was reported earlier as a novel potent competitive inhibitor, makes several hydrogen bonds with protein atoms, and the naphthyl moiety is located in the hydrophobic pocket. The inhibitor binding induces a disorder in one of the loops near the active site. In both crystal forms, GluR exists as a dimer and the interactions seen at the dimer interface are almost identical. This agrees well with the results from gel filtration and dynamic light-scattering studies.


    Organizational Affiliation

    Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-Dong, Sungbuk-Gu, Seoul, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate Racemase
A
264Streptococcus pyogenes serotype M1Gene Names: murI (glr)
EC: 5.1.1.3
Find proteins for Q9A1B7 (Streptococcus pyogenes serotype M1)
Go to UniProtKB:  Q9A1B7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHL
Query on NHL

Download SDF File 
Download CCD File 
A
(4S)-4-(2-NAPHTHYLMETHYL)-D-GLUTAMIC ACID
GAMMA-2-NAPHTHYLMETHYL-D-GLUTAMIC ACID
C16 H17 N O4
YDWIUFASTTZKNI-UONOGXRCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NHLKi: 16 nM BINDINGMOAD
NHLIC50: 350 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.226 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.745α = 90.00
b = 79.745β = 90.00
c = 95.700γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-01-10 
  • Released Date: 2007-09-25 
  • Deposition Author(s): Kim, E.E.

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance