1SFT

ALANINE RACEMASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 1329-1342

  • DOI: 10.1021/bi961856c
  • Primary Citation of Related Structures:  
    1SFT

  • PubMed Abstract: 
  • The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, which includes residues 1-240, and a C-terminal domain essentially composed of beta-strand (residues 241-388) ...

    The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, which includes residues 1-240, and a C-terminal domain essentially composed of beta-strand (residues 241-388). In the structure of the dimer the mouth of the alpha/beta barrel of one monomer faces the second domain of the other monomer. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to Lys39, which is at the C-terminus of the first beta-strand of the alpha/beta barrel. This is the first example of a PLP cofactor binding in the active site of a alpha/beta barrel. A number of other residues are involved in maintaining the position of the PLP in the protein. Of these, Arg219 is the most interesting, as it forms a hydrogen bond with the pyridine nitrogen of the cofactor. This is the first known occurrence of such an interaction with PLP and is expected to influence the electron delocalization in the PLP-alanine intermediates. A second arginine residue, Arg136, donates a hydrogen bond to the phenolic oxygen of PLP and may be involved in the binding of substrate as well as stabilization of intermediates. Finally, Tyr265', from the second monomer, is postulated to be 2 proton donor to the carbanion intermediate.


    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

    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
ALANINE RACEMASE AB388Geobacillus stearothermophilusMutation(s): 0 
Gene Names: alrdal
EC: 5.1.1.1
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
Query on PLP

Download Ideal Coordinates CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.59α = 90
b = 90.13β = 90
c = 85.13γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance