PDBsum entry 3daa

Aminotransferase

PDB id: 3daa

Contents

Protein chains

277 a.a. *

Ligands

PDD ×2

Waters ×253

* Residue conservation analysis

PDB id:

3daa

Name:

Aminotransferase

Title:

Crystallographic structure of d-amino acid aminotransferase inactivated by pyridoxyl-d-alanine

Structure:

D-amino acid aminotransferase. Chain: a, b. Engineered: yes

Source:

Bacillus sp.. Organism_taxid: 72579. Strain: ym-1. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PDB file)

Resolution:

1.90Å R-factor: 0.195 R-free: 0.245

Authors:

D.Peisach,D.M.Chipman,D.Ringe

Key ref:

D.Peisach et al. (1998). Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase. Biochemistry, 37, 4958-4967. PubMed id: 9538014 DOI: 10.1021/bi972884d

Date:

20-Jan-98 Release date: 29-Apr-98

Protein chains

P19938  (DAAA_BACYM) -  D-alanine aminotransferase from Bacillus sp. (strain YM-1)

Seq: 283 a.a.

Struc: 277 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.21 - D-amino-acid transaminase.
• Reaction: D-alanine + 2-oxoglutarate = D-glutamate + pyruvate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PDD) matches with 68.18% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi972884d

Biochemistry 37:4958-4967 (1998)

PubMed id: 9538014

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

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

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.