PDBsum entry 1oat

Aminotransferase

PDB id: 1oat

Contents

Protein chain

404 a.a. *

Ligands

PLP ×3

Waters ×426

* Residue conservation analysis

PDB id:

1oat

Name:

Aminotransferase

Title:

Ornithine aminotransferase

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: oat. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Tetramer (from PDB file)

Resolution:

2.50Å R-factor: 0.185 R-free: 0.235

Authors:

B.W.Shen,T.Schirmer,J.N.Jansonius

Key ref:

B.W.Shen et al. (1998). Crystal structure of human recombinant ornithine aminotransferase. J Mol Biol, 277, 81. PubMed id: 9514741 DOI: 10.1006/jmbi.1997.1583

Date:

26-Mar-97 Release date: 01-Apr-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 = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1006/jmbi.1997.1583

J Mol Biol 277:81 (1998)

PubMed id: 9514741

Crystal structure of human recombinant ornithine aminotransferase.

B.W.Shen, M.Hennig, E.Hohenester, J.N.Jansonius, T.Schirmer.

ABSTRACT

Ornithine aminotransferase (OAT), a pyridoxal-5'-phosphate dependent enzyme, catalyses the transfer of the delta-amino group of L-ornithine to 2-oxoglutarate, producing L-glutamate-gamma-semialdehyde, which spontaneously cyclizes to pyrroline-5-carboxylate, and L-glutamate. The crystal structure determination of human recombinant OAT is described in this paper. As a first step, the structure was determined at low resolution (6 A) by molecular replacement using the refined structure of dialkylglycine decarboxylase as a search model. Crystallographic phases were then refined and extended in a step-wise fashion to 2.5 A by cyclic averaging of the electron density corresponding to the three monomers within the asymmetric unit. Interpretation of the resulting map was straightforward and refinement of the model resulted in an R-factor of 17.1% (Rfree=24.3%). The success of the procedure demonstrates the power of real-space molecular averaging even with only threefold redundancy. The alpha6-hexameric molecule is a trimer of intimate dimers with a monomer-monomer interface of 5500 A2 per subunit. The three dimers are related by an approximate 3-fold screw axis with a translational component of 18 A. The monomer fold is that of a typical representative of subgroup 2 aminotransferases and very similar to those described for dialkylglycine decarboxylase from Pseudomonas cepacia and glutamate-1-semialdehyde aminomutase from Synechococcus. It consists of a large domain that contributes most to the subunit interface, a C-terminal small domain most distant to the 2-fold axis and an N-terminal region that contains a helix, a loop and a three stranded beta-meander embracing a protrusion in the large domain of the second subunit of the dimer. The large domain contains the characteristic central seven-stranded beta-sheet (agfedbc) covered by eight helices in a typical alpha/beta fold. The cofactor pyridoxal-5'-phosphate is bound through a Schiff base to Lys292, located in the loop between strands f and g. The C-terminal domain includes a four-stranded antiparallel beta-sheet in contact with the large domain and three further helices at the far end of the subunit. The active sites of the dimer lie, about 25 A apart, at the subunit and domain interfaces. The conical entrances are on opposite sides of the dimer. In the active site, R180, E235 and R413 are probable substrate binding residues. Structure-based sequence comparisons with related transaminases in this work support that view. In patients suffering from gyrate atrophy, a recessive hereditary genetic disorder that can cause blindness in humans, ornithine aminotransferase activity is lacking. A large number of frameshift and point mutations in the ornithine aminotransferase gene have been identified in such patients. Possible effects of the various point mutations on the structural stability or the catalytic competence of the enzyme are discussed in light of the three-dimensional structure.

Selected figure(s)

Figure 8.
Figure 8. Molecular surface representation of the hexameric structure of OAT. The monomers (shown in different colors and labeled) form three tight dimers (AB, CC′, A′B′) that are related by a pseudo-3-fold screw axis with a translation component of 18 Å. The screw-axis and the three molecular dyads are shown in magenta. (a) View along the screw axis. The vertical dyad is crystallographic and relates C with C′ as well as dimer AB with dimer A′B′. The two other dyads are non-crystallographic. (b) View along the crystallographic dyad and perpendicular to the pseudo-3-fold screw axis. The figures were produced using program GRASP [Nicholls et al 1991].

Figure 10.
Figure 10. Stereo view of the superimposed C^α-traces of the refined monomer models of OAT (black) and DGD (red). The molecular dyad is shown in green. The large insertion in the DGD structure (loops at the lower-left) is responsible for tetramer formation [Toney et al 1995a]. The Figure was produced using GRASP [Nicholls et al 1991].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 277, 81-0) copyright 1998.

Figures were selected by an automated process.