Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 36.01 kDa 
• Atom Count: 2514 
• Modelled Residue Count: 320 
• Deposited Residue Count: 320 
• Unique protein chains: 1

1FB5

LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE

• PDB DOI: 10.2210/pdb1FB5/pdb

• Classification: TRANSFERASE
• Organism(s): Ovis aries
• Mutation(s): No 


• Deposited: 2000-07-14 Released: 2003-08-26 
• Deposition Author(s): Zanotti, G., Battistutta, R., Panzalorto, M., Francescato, P., Bruno, G., De Gregorio, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.219 

Literature

Functional and structural characterization of ovine ornithine transcarbamoylase.

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

(2003) Org Biomol Chem 1: 3178-3185

• PubMed: 14527149 
• DOI: 10.1039/b304901a
• Primary Citation of Related Structures:  
  1FB5


• PubMed 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.

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Related Citations: 

• 1.85 A Resolution Crystal Structure of Human Ornithine Transcarbamoylase Complexed with N-phopshonacetyl-L-ornithine. Catalytic Mechanism and Correlation with Inherited Deficiency.
  Shi, D., Morizono, H., Ha, Y., Aoyagi, M., Tuchman, M., Allewell, N.M.
  (1998) J Biol Chem 273: 34247

• Substrate-induced Conformational Change in a Trimeric Ornithine Transcarbamoylase
  Ha, Y., McCann, M.T., Tuchman, M., Allewell, N.M.
  (1997) Proc Natl Acad Sci U S A 94: 9550

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Organizational Affiliation: 

Department of Organic and Biological Chemistry, University of Messina, Salita Sperone 31, 98166 Messina, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORNITHINE TRANSCARBAMOYLASE	A	320	Ovis aries	Mutation(s): 0  Gene Names: OTC EC: 2.1.3.3
UniProt
Find proteins for P84010 (Ovis aries) Explore P84010  Go to UniProtKB:  P84010

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NVA	B [auth A]	NORVALINE C5 H11 N O2 SNDPXSYFESPGGJ-BYPYZUCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.219 
• Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.7	α = 90
b = 184.7	β = 90
c = 184.7	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-14 
• Released Date: 2003-08-26 
Deposition Author(s): Zanotti, G., Battistutta, R., Panzalorto, M., Francescato, P., Bruno, G., De Gregorio, A.

Revision History  

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance