PDBsum entry 2oat

Aminotransferase

PDB id: 2oat

Contents

Protein chain

404 a.a. *

Ligands

PFM ×3

Waters ×744

* Residue conservation analysis

PDB id:

2oat

Name:

Aminotransferase

Title:

Ornithine aminotransferase complexed with 5-fluoromethylornithine

Structure:

Ornithine aminotransferase. Chain: a, b, c. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: liver. Organelle: mitochondria. Cellular_location: intramitochondria. Gene: oat. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Tetramer (from PDB file)

Resolution:

1.95Å R-factor: 0.206 R-free: 0.232

Authors:

P.Storici,T.Schirmer

Key ref:

P.Storici et al. (1999). Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine. J Mol Biol, 285, 297-309. PubMed id: 9878407 DOI: 10.1006/jmbi.1998.2289

Date:

07-May-98 Release date: 09-Dec-98

Protein chains

P04181  (OAT_HUMAN) -  Ornithine aminotransferase, mitochondrial from Homo sapiens

Seq: 439 a.a.

Struc: 404 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.13 - ornithine aminotransferase.
• Reaction: a 2-oxocarboxylate + L-ornithine = L-glutamate 5-semialdehyde + an L-alpha-amino acid
• Cofactor: Pyridoxal 5'-phosphate

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

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

reference

DOI no: 10.1006/jmbi.1998.2289

J Mol Biol 285:297-309 (1999)

PubMed id: 9878407

Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine.

P.Storici, G.Capitani, R.Müller, T.Schirmer, J.N.Jansonius.

ABSTRACT

Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC 2.6.1.13), a pyridoxal-5'-phosphate-dependent mitochondrial enzyme controls the l-ornithine level in tissues by catalyzing the transfer of the delta-amino group of l-ornithine to 2-oxoglutarate, producing l-glutamate- gamma-semialdehyde and l-glutamate. (2S, 5S)-5-Fluoromethylornithine is the only inhibitor exclusively specific for ornithine aminotransferase known to date. Both in vitro and in vivo, it blocks the enzyme by a suicide reaction leading to a covalent adduct with the cofactor. The crystal structure of the enzyme-inhibitor complex was solved at a resolution of 1.95 A. No significant conformational changes compared with the native enzyme structure were observed. The structure reveals the atomic details of the cofactor-inhibitor adduct and its interactions with the active site of the enzyme. The main residues responsible for specific binding of the inhibitor are Arg180, which forms a strong salt bridge with the alpha-carboxylate and Tyr55, which is involved in a short hydrogen bond with the alpha-amino group. The experimental observation that in the racemic mixture, (2S, 5S)-5-fluoromethylornithine is exclusively responsible for the enzyme inhibition can be explained on the basis of the active site topology. Model building studies strongly suggest that the natural substrate l-ornithine, in its external aldimine adduct with the enzyme, makes use of the same recognition site as the inhibitor. It is proposed that the neutralization of the active site Arg413 by a salt bridge with Glu235 also plays an important role in productive binding of both 5-fluoromethylornithine and l-ornithine. Arg180 and Arg413 are believed to be instrumental in recognition of l-glutamate, by binding its gamma and alpha-carboxylate groups, respectively. This requires a different side-chain conformation of Glu235. Lys292 is the only obvious candidate for catalyzing the rate-limiting proton transfer steps in the transamination reaction.

Selected figure(s)

Figure 2.
Figure 2. Structural formulas of (a) ornithine (Orn) and (b) 5-fluoromethylornithine (6-fluoro-2,5-diamino- hexanoic acid, 5FMOrn).

Figure 3.
Figure 3. Schematic drawing of the reactants and the product of the inhibition reaction (Bolkenius et al., 1990). 5FMOrn reacts with the cofactor-K292 internal aldimine and, via a multistep reaction (see the text for more detail), a stable adduct with PLP is formed. This is an unsaturated ketone with an absorption maximum at 458 nm. The sys- tematic name of this molecule is 2-ammonio-7-(2-methyl-3-oxido-5-((phosphonoxy)-methyl)-4-pyridoxyl-5-oxo-6-hep- tenoate. For simplicity, we refer to it as FMP.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 285, 297-309) copyright 1999.

Figures were selected by an automated process.