PDBsum entry 1fb5

Transferase

PDB id: 1fb5

Contents

Protein chain

320 a.a. *

Ligands

NVA

Waters ×3

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Functional and structural characterization of ovine ornithine transcarbamoylase.

Authors

A.De gregorio, R.Battistutta, N.Arena, M.Panzalorto, P.Francescato, G.Valentini, G.Bruno, G.Zanotti.

Ref.

Org Biomol Chem, 2003, 1, 3178-3185.

PubMed id

14527149

Abstract

Ornithine transcarbamoylase from ovine liver has been purified to homogeneity. Like all anabolic OTCs, the ovine enzyme is a trimer, constituted by identical subunits of 34 kDa. Sequence analysis of the 54 N-terminal residues of ovine OTC shows a high degree of homology with the human enzyme. The optimum pH and the Michaelis constants for the catalytic reaction were determined. The ovine enzyme is the most thermostable one among mammals OTCs, its critical temperature being 6 degrees C higher than those measured for the other enzymes. The enzyme has been crystallised and the structure determined at 3.5 A resolution. Crystals belong to the cubic P4(3)32 space group, with a = b = c = 184.7 A and a solvent content of about 80%. There is no evidence of any ligand in the active site cavity, indicating that the crystals contain an unliganded or T state of the enzyme. The unliganded OTCase enzyme adopts a trimeric structure which, in the crystal, presents a three-fold axis coincident with the crystallographic one. The conformation of each monomer in the trimer is quite similar to that of the liganded human protein, with the exception of a few loops, directly interacting with the substrate(s), which are able to induce a rearrangement of the quaternary organisation of the trimer, that accounts for the cooperative behaviour of the enzyme following the binding of the substrates.

Secondary reference #1

Title

1.85-A resolution crystal structure of human ornithine transcarbamoylase complexed with n-Phosphonacetyl-L-Ornithine. Catalytic mechanism and correlation with inherited deficiency.

Authors

D.Shi, H.Morizono, Y.Ha, M.Aoyagi, M.Tuchman, N.M.Allewell.

Ref.

J Biol Chem, 1998, 273, 34247-34254. [DOI no: 10.1074/jbc.273.51.34247]

PubMed id

9852088

Figure 5.
Fig. 5. Stereo view (upper panel) and schematic (lower panel) showing the interaction of the bisubstrate analog PALO with active site residues. PALO is shown in bold. The residue indicated with * is from an adjacent subunit.

Figure 10.
Fig. 10. Location of some deletereious OTCD mutations, shown as colored spheres: mutations at and near active site (red), mutations involving proline (green), mutations in the protein core (blue), mutations at inter-domain interface (purple), mutations at intersubunit interface (yellow), and mutations on convex face of trimer (cyan). PALO is shown as a ball-stick model.

The above figures are reproduced from the cited reference with permission from the ASBMB

Secondary reference #2

Title

Substrate-Induced conformational change in a trimeric ornithine transcarbamoylase.

Authors

Y.Ha, M.T.Mccann, M.Tuchman, N.M.Allewell.

Ref.

Proc Natl Acad Sci U S A, 1997, 94, 9550-9555. [DOI no: 10.1073/pnas.94.18.9550]

PubMed id

9275160

Figure 3.
Fig. 3. Cartoon drawings of E. coli OTCase catalytic trimer ligated with the bisubstrate analog PALO, shown as a space filling model. These figures were generated by graphic programs MOLSCRIPT (57) and RENDER (58, 59). Chain A1, A2, and A3 are colored light blue, blue, and green respectively. (Upper) Top view, down the^ molecular three-fold axis. CP and L-ornithine binding domains of chain A1 are labeled. One active site, shared between chain A1 and the 80s loop of chain A2, is also labeled. (Lower) Side^ view, perpendicular to the three-fold axis. N/C termini and helices 1, 7, 8a, and 9a of chain A2 are labeled.

Figure 4.
Fig. 4. Stereoview showing the interaction of the bisubstrate analog PALO with active site residues and interactions of Arg-57 and^ PALO with Gln-82, Lys-86, and Glu-87 of the 80s loop from an adjacent polypeptide chain. The interactions between NZ of Lys-86 with OE1 of Gln-82 and OT1 of PALO appear to be bridged by disordered^ water molecules.