PDBsum entry 2dab

Transferase

PDB id: 2dab

Contents

Protein chains

280 a.a. *

Ligands

PLP ×2

Waters ×166

* Residue conservation analysis

PDB id:

2dab

Name:

Transferase

Title:

L201a mutant of d-amino acid aminotransferase complexed with pyridoxal-5'-phosphate

Structure:

D-amino acid aminotransferase. Chain: a, b. Synonym: d-alanine aminotransferase, d-aspartate aminotransferase. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.218 R-free: 0.273

Authors:

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

Key ref:

S.Sugio et al. (1998). Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. Protein Eng, 11, 613-619. PubMed id: 9749913

Date:

30-Nov-97 Release date: 03-Jun-98

Protein chains

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

Seq: 283 a.a.

Struc: 280 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 = PLP) matches with 93.75% similarity)

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

reference

Protein Eng 11:613-619 (1998)

PubMed id: 9749913

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

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

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 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.