2SFP

ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.

Morollo, A.A.Petsko, G.A.Ringe, D.

(1999) Biochemistry 38: 3293-3301

  • DOI: 10.1021/bi9822729

  • PubMed Abstract: 
  • The structure of alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a ...

    The structure of alanine racemase from Bacillus stearothermophilus with the inhibitor propionate bound in the active site was determined by X-ray crystallography to a resolution of 1.9 A. The enzyme is a homodimer in solution and crystallizes with a dimer in the asymmetric unit. Both active sites contain a pyridoxal 5'-phosphate (PLP) molecule in aldimine linkage to Lys39 as a protonated Schiff base, and the pH-independence of UV-visible absorption spectra suggests that the protonated PLP-Lys39 Schiff base is the reactive form of the enzyme. The carboxylate group of propionate bound in the active site makes numerous interactions with active-site residues, defining the substrate binding site of the enzyme. The propionate-bound structure therefore approximates features of the Michaelis complex formed between alanine racemase and its amino acid substrate. The structure also provides evidence for the existence of a carbamate formed on the side-chain amino group of Lys129, stabilized by interactions with one of the residues interacting with the carboxylate group of propionate, Arg136. We propose that this novel interaction influences both substrate binding and catalysis by precisely positioning Arg136 and modulating its charge.


    Related Citations: 
    • Reaction of Alanine Racemase with 1-Aminoethylphosphonic Acid Forms a Stable External Aldimine Intermediate
      Stamper, C.G.,Morollo, A.A.,Ringe, D.
      (1998) Biochemistry 37: 10438
    • Determination of the Structure of Alanine Racemase from Bacillus Stearothermophilus at 1.9 Angstroms Resolution
      Shaw, J.P.,Petsko, G.A.,Ringe, D.
      (1997) Biochemistry 36: 1329
    • 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.,Soad, K.,Walsh, C.T.,Petsko, G.A.
      (1987) J.Biol.Chem. 262: 15323


    Organizational Affiliation

    Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ALANINE RACEMASE)
A, B
388Geobacillus stearothermophilusMutation(s): 0 
Gene Names: alr (dal)
EC: 5.1.1.1
Find proteins for P10724 (Geobacillus stearothermophilus)
Go to UniProtKB:  P10724
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PPI
Query on PPI

Download SDF File 
Download CCD File 
A, B
PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PPIKi: 20000000 nM BINDINGMOAD
PPIKi: 20000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.700α = 90.00
b = 90.000β = 90.00
c = 85.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance