Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.08 kDa 
• Atom Count: 4761 
• Modelled Residue Count: 554 
• Deposited Residue Count: 554 
• Unique protein chains: 1

3DAA

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

• PDB DOI: 10.2210/pdb3DAA/pdb

• Classification: AMINOTRANSFERASE
• Organism(s): Bacillus sp. YM-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-01-20 Released: 1998-04-29 
• Deposition Author(s): Peisach, D., Chipman, D.M., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

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

• PubMed: 9538014 
• DOI: 10.1021/bi972884d
• Primary Citation of Related Structures:  
  3DAA, 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-AMINO ACID AMINOTRANSFERASE	A, B	277	Bacillus sp. YM-1	Mutation(s): 0  Gene Names: dat EC: 2.6.1.21
UniProt
Find proteins for P19938 (Bacillus sp. (strain YM-1)) Explore P19938  Go to UniProtKB:  P19938

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PDD	C [auth A], D [auth B]	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE C11 H17 N2 O7 P WACJCHFWJNNBPR-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.1	α = 90
b = 78.3	β = 90
c = 88.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-01-20 
• Released Date: 1998-04-29 
Deposition Author(s): Peisach, D., Chipman, D.M., Ringe, D.

Revision History  

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