1A0G

L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAMINE-5'-PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination.

Sugio, S.Kashima, A.Kishimoto, K.Peisach, D.Petsko, G.A.Ringe, D.Yoshimura, T.Esaki, N.

(1998) Protein Eng. 11: 613-619

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The leucine-to-alanine mutation at residue 201 of D-amino acid aminotransferase provides a unique enzyme which gradually loses its activity while catalyzing the normal transamination; the co-enzyme form is converted from pyridoxal 5'-phosphate to pyr ...

    The leucine-to-alanine mutation at residue 201 of D-amino acid aminotransferase provides a unique enzyme which gradually loses its activity while catalyzing the normal transamination; the co-enzyme form is converted from pyridoxal 5'-phosphate to pyridoxamine 5'-phosphate upon the inactivation [Kishimoto,K., Yoshimura,T., Esaki,N., Sugio,S., Manning,J.M. and Soda,K. (1995) J. Biochem., 117, 691-696]. Crystal structures of both co-enzyme forms of the mutant enzyme have been determined at 2.0 A resolution: they are virtually identical, and are quite similar to that of the wild-type enzyme. Significant differences in both forms of the mutant are localized only on the bound co-enzyme, the side chains of Lys145 and Tyr31, and a water molecule sitting on the putative substrate binding site. Detailed comparisons of the structures of the mutant, together with that of the pyridoxamine-5'-phosphate form of the wild-type enzyme, imply that Leu201 would play a crucial role in the transamination reaction by keeping the pyridoxyl ring in the proper location without disturbing its oscillating motion, although the residue seems to not be especially important for the structural integrity of the enzyme.


    Related Citations: 
    • Crystal Structure of a D-Amino Acid Aminotransferase: How the Protein Controls Stereoselectivity
      Sugio, S.,Petsko, G.A.,Manning, J.M.,Soda, K.,Ringe, D.
      (1995) Biochemistry 34: 9661
    • Role of Leucine 201 of Thermostable D-Amino Acid Aminotransferase from a Thermophile, Bacillus Sp. Ym-1
      Kishimoto, K.,Yoshimura, T.,Esaki, N.,Sugio, S.,Manning, J.M.,Soda, K.
      (1995) J.Biochem.(Tokyo) 117: 691


    Organizational Affiliation

    The Green Cross Corporation, Hirakata, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-AMINO ACID AMINOTRANSFERASE
A, B
282Bacillus sp. (strain YM-1)Mutation(s): 1 
Gene Names: dat
EC: 2.6.1.21
Find proteins for P19938 (Bacillus sp. (strain YM-1))
Go to UniProtKB:  P19938
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP
Query on PMP

Download SDF File 
Download CCD File 
A, B
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.340α = 90.00
b = 91.760β = 90.00
c = 88.690γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata reduction
X-PLORmodel building
X-PLORrefinement
PROCESSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance