1BD0

ALANINE RACEMASE COMPLEXED WITH ALANINE PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine.

Stamper, G.F.Morollo, A.A.Ringe, D.Stamper, C.G.

(1998) Biochemistry 37: 10438-10445

  • DOI: 10.1021/bi980692s

  • PubMed Abstract: 
  • (R)-1-Aminoethylphosphonic acid (L-Ala-P), a synthetic L-alanine analogue, has antibacterial activity and is a time-dependent inactivator of all purified Gram-positive bacterial alanine racemases that have been tested. L-Ala-P forms an external aldim ...

    (R)-1-Aminoethylphosphonic acid (L-Ala-P), a synthetic L-alanine analogue, has antibacterial activity and is a time-dependent inactivator of all purified Gram-positive bacterial alanine racemases that have been tested. L-Ala-P forms an external aldimine with the bound pyridoxal 5'-phosphate (PLP) cofactor, but is neither racemized nor efficiently hydrolyzed. To understand the structural basis of the inactivation of the enzyme by L-Ala-P, we determined the crystal structure of the complex between L-Ala-P and alanine racemase at 1.6 A resolution. The cofactor derivative in the inhibited structure tilts outward from the protein approximately 20 degrees relative to the internal aldimine. The phosphonate oxygens are within hydrogen bonding distance of four amino acid residues and two water molecules in the active site of the enzyme. L-Ala-P is an effective inhibitor of alanine racemase because, upon formation of the external aldimine, the phosphonate group interacts with putative catalytic residues, thereby rendering them unavailable for catalysis. Furthermore, this aldimine appears to be inappropriately aligned for efficient Calpha proton abstraction. The combination of these effects leads to a stable aldimine derivative and potent inactivation of alanine racemase by this compound.


    Related Citations: 
    • X-Ray Crystallographic Studies of the Alanine-Specific Racemase from Bacillus Stearothermophilus. Overproduction, Crystallization, and Preliminary Characterization
      Neidhart, D.J.,Distefano, M.D.,Tanizawa, K.,Soda, K.,Walsh, C.T.,Petsko, G.A.
      (1987) J.Biol.Chem. 262: 15323
    • Determination of the Structure of Alanine Racemase from Bacillus Stearothermophilus at 1.9-A Resolution
      Shaw, J.P.,Petsko, G.A.,Ringe, D.
      (1997) Biochemistry 36: 1329


    Organizational Affiliation

    Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALANINE RACEMASE
A, B
388Geobacillus stearothermophilusGene Names: alr (dal)
EC: 5.1.1.1
Find proteins for P10724 (Geobacillus stearothermophilus)
Go to UniProtKB:  P10724
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IN5
Query on IN5

Download SDF File 
Download CCD File 
A, B
{1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID
C10 H18 N2 O8 P2
WHDCJKAOZPBUAY-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.227α = 90.00
b = 87.690β = 90.00
c = 85.305γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance