2SFP

ALANINE RACEMASE WITH BOUND PROPIONATE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    2SFP

  • 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 dimer in the asymmetric unit ...

    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.
      Stamper, G.F., Morollo, A.A., Ringe, D., Stamper, C.G.
      (1998) Biochemistry 37: 10438
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ALANINE RACEMASE)A, B388Geobacillus stearothermophilusMutation(s): 0 
Gene Names: alrdal
EC: 5.1.1.1
UniProt
Find proteins for P10724 (Geobacillus stearothermophilus)
Explore P10724 
Go to UniProtKB:  P10724
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
PPI
Query on PPI

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]PROPANOIC ACID
C3 H6 O2
XBDQKXXYIPTUBI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, BL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
PPI PDBBind:  2SFP Ki: 2.00e+7 (nM) from 1 assay(s)
Binding MOAD:  2SFP Ki: 2.00e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.7α = 90
b = 90β = 90
c = 85.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references, Derived calculations