1FB5

LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORNITHINE TRANSCARBAMOYLASEA320Ovis ariesMutation(s): 0 
Gene Names: OTC
EC: 2.1.3.3
UniProt
Find proteins for P84010 (Ovis aries)
Explore P84010 
Go to UniProtKB:  P84010
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84010
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NVA
Query on NVA

Download Ideal Coordinates CCD File 
B [auth A]NORVALINE
C5 H11 N O2
SNDPXSYFESPGGJ-BYPYZUCNSA-N
 Ligand Interaction
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 = 184.7α = 90
b = 184.7β = 90
c = 184.7γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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