1L6F

Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.

Watanabe, A.Yoshimura, T.Mikami, B.Hayashi, H.Kagamiyama, H.Esaki, N.

(2002) J.Biol.Chem. 277: 19166-19172

  • DOI: 10.1074/jbc.M201615200
  • Primary Citation of Related Structures:  1L6G

  • PubMed Abstract: 
  • The crystal structures of alanine racemase bound with reaction intermediate analogs, N-(5'-phosphopyridoxyl)-L-alanine (PLP-L-Ala) and N-(5'-phosphopyridoxyl)-D-alanine (PLP-D-Ala), were determined at 2.0-A resolution with the crystallographic R fact ...

    The crystal structures of alanine racemase bound with reaction intermediate analogs, N-(5'-phosphopyridoxyl)-L-alanine (PLP-L-Ala) and N-(5'-phosphopyridoxyl)-D-alanine (PLP-D-Ala), were determined at 2.0-A resolution with the crystallographic R factor of 17.2 for PLP-L-Ala and 16.9 for PLP-D-Ala complexes. They were quite similar not only to each other but also to the structure of the native pyridoxal 5'-phosphate (PLP)-form enzyme; root mean square deviations at Calpha among the three structures were less than 0.28 A. The side chains of the amino acid residues around the PLP-L-Ala and PLP-D-Ala were virtually superimposable on each other as well as on those around PLP of the native holoenzyme. The alpha-hydrogen of the alanine moiety of PLP-L-Ala was located near the OH of Tyr(265)', whereas that of PLP-D-Ala was near the NZ of Lys(39). These support the previous findings that Tyr(265)' and Lys(39) are the catalytic bases removing alpha-hydrogen from L- and D-alanine, respectively. The prerequisite for this two-base mechanism is that the alpha-proton abstracted from the substrate is transferred (directly or indirectly) between the NZ of Lys(39) and the OH of Tyr(265'); otherwise the enzyme reaction stops after a single turnover. Only the carboxylate oxygen atom of either PLP-Ala enantiomer occurred at a reasonable position that can mediate the proton transfer; neither the amino acid side chains nor the water molecules were located in the vicinity. Therefore, we propose a mechanism of alanine racemase reaction in which the substrate carboxyl group directly participates in the catalysis by mediating the proton transfer between the two catalytic bases, Lys(39) and Tyr(265)'. The results of molecular orbital calculation also support this mechanism.


    Related Citations: 
    • Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a stable external aldimine
      Stamper, G.F.,Morollo, A.A.,Ringe, D.
      (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
    • 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


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.




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
PP3
Query on PP3

Download SDF File 
Download CCD File 
A, B
ALANYL-PYRIDOXAL-5'-PHOSPHATE
PYRIDOXYL-ALANINE-5-PHOSPHATE; VITAMIN B6 COMPLEXED WITH ALANINE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-ZETCQYMHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.960α = 90.00
b = 90.866β = 90.00
c = 85.417γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-05
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance