1OTH

CRYSTAL STRUCTURE OF HUMAN ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ORNITHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

1.85-A resolution crystal structure of human ornithine transcarbamoylase complexed with N-phosphonacetyl-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: 34247-34254

  • DOI: 10.1074/jbc.273.51.34247
  • Primary Citation of Related Structures:  
    1OTH

  • PubMed Abstract: 
  • The crystal structure of human ornithine transcarbamoylase complexed with the bisubstrate analog N-phosphonacetyl-L-ornithine has been solved at 1.85-A resolution by molecular replacement. Deleterious mutations produce clinical hyperammonia that, if untreated, results in neurological symptoms or death (ornithine transcarbamylase deficiency) ...

    The crystal structure of human ornithine transcarbamoylase complexed with the bisubstrate analog N-phosphonacetyl-L-ornithine has been solved at 1.85-A resolution by molecular replacement. Deleterious mutations produce clinical hyperammonia that, if untreated, results in neurological symptoms or death (ornithine transcarbamylase deficiency). The holoenzyme is trimeric, and as in other transcarbamoylases, each subunit contains an N-terminal domain that binds carbamoyl phosphate and a C-terminal domain that binds L-ornithine. The active site is located in the cleft between domains and contains additional residues from an adjacent subunit. Binding of N-phosphonacetyl-L-ornithine promotes domain closure. The resolution of the structure enables the role of active site residues in the catalytic mechanism to be critically examined. The side chain of Cys-303 is positioned so as to be able to interact with the delta-amino group of L-ornithine which attacks the carbonyl carbon of carbamoyl phosphate in the enzyme-catalyzed reaction. This sulfhydryl group forms a charge relay system with Asp-263 and the alpha-amino group of L-ornithine, instead of with His-302 and Glu-310, as previously proposed. In common with other ureotelic ornithine transcarbamoylases, the human enzyme lacks a loop of approximately 20 residues between helix H10 and beta-strand B10 which is present in prokaryotic ornithine transcarbamoylases but has a C-terminal extension of 10 residues that interacts with the body of the protein but is exposed. The sequence of this C-terminal extension is homologous to an interhelical loop found in several membrane proteins, including mitochondrial transport proteins, suggesting a possible mode of interaction with the inner mitochondrial membrane.


    Organizational Affiliation

    Department of Biochemistry, University of Minnesota, St. Paul, Minnesota 55108, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ORNITHINE TRANSCARBAMOYLASE)A321Homo sapiensMutation(s): 0 
Gene Names: OTC
EC: 2.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00480 (Homo sapiens)
Explore P00480 
Go to UniProtKB:  P00480
PHAROS:  P00480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00480
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAO
Query on PAO

Download Ideal Coordinates CCD File 
B [auth A]N-(PHOSPHONOACETYL)-L-ORNITHINE
C7 H15 N2 O6 P
FCIHAQFHXJOLIF-YFKPBYRVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PAO PDBBind:  1OTH Ki: 100 (nM) from 1 assay(s)
BindingDB:  1OTH Ki: min: 100, max: 200 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.9α = 90
b = 125.9β = 90
c = 125.9γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-06
    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