2OTC

ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-(PHOSPHONACETYL)-L-ORNITHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate-induced conformational change in a trimeric ornithine transcarbamoylase.

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

(1997) Proc.Natl.Acad.Sci.USA 94: 9550-9555

  • DOI: 10.1073/pnas.94.18.9550

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli ornithine transcarbamoylase (OTCase, EC 2.1.3.3) complexed with the bisubstrate analog N-(phosphonacetyl)-L-ornithine (PALO) has been determined at 2.8-A resolution. This research on the structure of a transc ...

    The crystal structure of Escherichia coli ornithine transcarbamoylase (OTCase, EC 2.1.3.3) complexed with the bisubstrate analog N-(phosphonacetyl)-L-ornithine (PALO) has been determined at 2.8-A resolution. This research on the structure of a transcarbamoylase catalytic trimer with a substrate analog bound provides new insights into the linkages between substrate binding, protein-protein interactions, and conformational change. The structure was solved by molecular replacement with the Pseudomonas aeruginosa catabolic OTCase catalytic trimer (Villeret, V., Tricot, C., Stalon, V. & Dideberg, O. (1995) Proc. Natl. Acad. Sci. USA 92, 10762-10766; Protein Data Bank reference pdb 1otc) as the model and refined to a crystallographic R value of 21.3%. Each polypeptide chain folds into two domains, a carbamoyl phosphate binding domain and an L-ornithine binding domain. The bound inhibitor interacts with the side chains and/or backbone atoms of Lys-53, Ser-55, Thr-56, Arg-57, Thr-58, Arg-106, His-133, Asn-167, Asp-231, Met-236, Leu-274, Arg-319 as well as Gln-82 and Lys-86 from an adjacent chain. Comparison with the unligated P. aeruginosa catabolic OTCase structure indicates that binding of the substrate analog results in closure of the two domains of each chain. As in E. coli aspartate transcarbamoylase, the 240s loop undergoes the largest conformational change upon substrate binding. The clinical implications for human OTCase deficiency are discussed.


    Organizational Affiliation

    Department of Biochemistry, College of Biological Sciences, University of Minnesota, St. Paul, MN 55108, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORNITHINE CARBAMOYLTRANSFERASE
A, B, C, D, E, F, G, H, I
333Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: argI
EC: 2.1.3.3
Find proteins for P04391 (Escherichia coli (strain K12))
Go to UniProtKB:  P04391
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAO
Query on PAO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I
N-(PHOSPHONOACETYL)-L-ORNITHINE
C7 H15 N2 O6 P
FCIHAQFHXJOLIF-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 104.030α = 86.99
b = 114.690β = 93.11
c = 93.780γ = 118.81
Software Package:
Software NamePurpose
XENGENdata reduction
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
XENGENdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-06-15 
  • Released Date: 1998-06-17 
  • Deposition Author(s): Ha, Y., Allewell, N.M.

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance