3E6E

Crystal structure of Alanine racemase from E.faecalis complex with cycloserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the alanine racemase from Enterococcus faecalis.

Priyadarshi, A.Lee, E.H.Sung, M.W.Nam, K.H.Lee, W.H.Kim, E.E.Hwang, K.Y.

(2009) Biochim.Biophys.Acta 1794: 1030-1040

  • DOI: 10.1016/j.bbapap.2009.03.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. T ...

    Alanine racemase (AlaR) is a bacterial enzyme that belongs to the fold-type III group of pyridoxal 5'-phosphate (PLP)-dependent enzymes. AlaR catalyzes the interconversion between L- and D-alanine, which is important for peptidoglycan biosynthesis. This enzyme is common in prokaryotes, but absent in eukaryotes, which makes it an attractive target for the design of new antibacterial drugs. Here, we report the crystal structures of both the apoenzyme and the d-cycloserine (DCS) complex of AlaR from the pathogenic bacterium Enterococcus faecalis v583, at a resolution of 2.5 A. DCS is a suicide inhibitor of AlaR and, as such, serves as an antimicrobial agent and has been used to treat tuberculosis and urinary tract infection-related diseases, and makes several hydrogen bonds with the conserved active site residues, Tyr44 and Ser207, respectively. The apoenzyme crystal structure of AlaR consists of three monomers in the asymmetric unit, including a polyethylene glycol molecule in the dimer interface that surrounds one of the His 293 residues and also sits close to one side of the His 293 residue in the opposite monomer. Our results provide structural insights into AlaR that may be used for the development of new antibiotics targeting the alanine racemase in pathogenic bacteria.


    Organizational Affiliation

    Biomedical Research Center, Life Science Division, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alanine racemase
A, B, C
371Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 1 
Gene Names: alr
EC: 5.1.1.1
Find proteins for Q837J0 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q837J0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCS
Query on DCS

Download SDF File 
Download CCD File 
A, B, C
D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE
C11 H16 N3 O7 P
NNRZSZJOQKAGTO-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 94.597α = 90.00
b = 156.186β = 90.00
c = 146.930γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
CNSphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance