PDBsum entry 1akc

Transferase(aminotransferase)

PDB id: 1akc

Contents

Protein chain

401 a.a. *

Ligands

PPE

Waters ×311

* Residue conservation analysis

PDB id:

1akc

Name:

Transferase(aminotransferase)

Title:

Structural basis for the catalytic activity of aspartate aminotransferase k258h lacking its pyridoxal-5'-phosphate-binding lysine residue

Structure:

Aspartate aminotransferase. Chain: a. Engineered: yes

Source:

Gallus gallus. Chicken. Organism_taxid: 9031. Organ: heart. Expressed in: unidentified. Expression_system_taxid: 32644

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.172

Authors:

V.N.Malashkevich,J.N.Jansonius

Key ref:

V.N.Malashkevich et al. (1995). Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue. Biochemistry, 34, 405-414. PubMed id: 7819232 DOI: 10.1021/bi00002a004

Date:

28-Feb-94 Release date: 31-Jul-94

Protein chain

P00508  (AATM_CHICK) -  Aspartate aminotransferase, mitochondrial from Gallus gallus

Seq: 423 a.a.

Struc: 401 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.6.1.1 - aspartate transaminase.
• Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PPE) matches with 57.69% similarity)

• Enzyme class 2: E.C.2.6.1.7 - kynurenine--oxoglutarate transaminase.

Pathway:

• Reaction: L-kynurenine + 2-oxoglutarate = kynurenate + L-glutamate + H2O
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PPE) matches with 57.69% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1021/bi00002a004

Biochemistry 34:405-414 (1995)

PubMed id: 7819232

Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking the pyridoxal 5'-phosphate-binding lysine residue.

V.N.Malashkevich, J.Jäger, M.Ziak, U.Sauder, H.Gehring, P.Christen, J.N.Jansonius.

ABSTRACT

Chicken mitochondrial and Escherichia coli aspartate aminotransferases K258H, in which the active site lysine residue has been exchanged for a histidine residue, retain partial catalytic competence [Ziak et al. (1993) Eur. J. Biochem. 211, 475-484]. Mutant PLP and PMP holoenzymes and the complexes of the latter (E. coli enzyme) with sulfate and 2-oxoglutarate, as well as complexes of the mitochondrial apoenzyme with N-(5'-phosphopyridoxyl)-L-aspartate or N-(5'-phosphopyridoxyl)-L-glutamate, were crystallized and analyzed by means of X-ray crystallography in order to examine how the side chain of histidine 258 can substitute as a general acid/base catalyst of the aldimine-ketimine tautomerization in enzymic transamination. The structures have been solved and refined at resolutions between 2.1 and 2.8 A. Both the closed and the open conformations, identical to those of the wild-type enzyme, were observed, indicating that the mutant enzymes of both species exhibit the same conformational flexibility as the wild-type enzymes, although in AspAT K258H the equilibrium is somewhat shifted toward the open conformation. The replacement of the active site K258 by a histidine residue resulted only in local structural adaptations necessary to accommodate the imidazole ring. The catalytic competence of the mutant enzyme, which in the forward half-reaction is 0.1% of that of the wild-type enzyme, suggests that the imidazole group is involved in the aldimine-ketimine tautomerization. However, the imidazole ring of H258 is too far away from C alpha and C4' of the coenzyme-substrate adduct for direct proton transfer, suggesting that the 1,3-prototropic shift is mediated by a water molecule. Although there is enough space for a water molecule in this area, it has not been detected. Dynamic fluctuations of the protein matrix might transiently open a channel, giving a water molecule fleeting access to the active site.