3DAA

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.

Peisach, D.Chipman, D.M.Van Ophem, P.W.Manning, J.M.Ringe, D.

(1998) Biochemistry 37: 4958-4967

  • DOI: 10.1021/bi972884d
  • Primary Citation of Related Structures:  4DAA

  • PubMed Abstract: 
  • The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external al ...

    The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.


    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


    Organizational Affiliation

    Program in Bioorganic Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02254-9110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-AMINO ACID AMINOTRANSFERASE
A, B
277Bacillus sp. (strain YM-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
PDD
Query on PDD

Download SDF File 
Download CCD File 
A, B
N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.100α = 90.00
b = 78.300β = 90.00
c = 88.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance