Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report

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Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine.

Storici, P.Capitani, G.Muller, R.Schirmer, T.Jansonius, J.N.

(1999) J.Mol.Biol. 285: 297-309

  • DOI: 10.1006/jmbi.1998.2289

  • PubMed Abstract: 
  • Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC, a pyridoxal-5'-phosphate-dependent mitochondrial enzyme controls the l-ornithine level in tissues by catalyzing the transfer of the delta-amino group of l-ornithi ...

    Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC, a pyridoxal-5'-phosphate-dependent mitochondrial enzyme controls the l-ornithine level in tissues by catalyzing the transfer of the delta-amino group of l-ornithine to 2-oxoglutarate, producing l-glutamate- gamma-semialdehyde and l-glutamate. (2S, 5S)-5-Fluoromethylornithine is the only inhibitor exclusively specific for ornithine aminotransferase known to date. Both in vitro and in vivo, it blocks the enzyme by a suicide reaction leading to a covalent adduct with the cofactor. The crystal structure of the enzyme-inhibitor complex was solved at a resolution of 1.95 A. No significant conformational changes compared with the native enzyme structure were observed. The structure reveals the atomic details of the cofactor-inhibitor adduct and its interactions with the active site of the enzyme. The main residues responsible for specific binding of the inhibitor are Arg180, which forms a strong salt bridge with the alpha-carboxylate and Tyr55, which is involved in a short hydrogen bond with the alpha-amino group. The experimental observation that in the racemic mixture, (2S, 5S)-5-fluoromethylornithine is exclusively responsible for the enzyme inhibition can be explained on the basis of the active site topology. Model building studies strongly suggest that the natural substrate l-ornithine, in its external aldimine adduct with the enzyme, makes use of the same recognition site as the inhibitor. It is proposed that the neutralization of the active site Arg413 by a salt bridge with Glu235 also plays an important role in productive binding of both 5-fluoromethylornithine and l-ornithine. Arg180 and Arg413 are believed to be instrumental in recognition of l-glutamate, by binding its gamma and alpha-carboxylate groups, respectively. This requires a different side-chain conformation of Glu235. Lys292 is the only obvious candidate for catalyzing the rate-limiting proton transfer steps in the transamination reaction.

    Related Citations: 
    • Crystal Structure of Human Recombinant Ornithine Aminotransferase
      Shen, B.W.,Hennig, M.,Hohenester, E.,Jansonius, J.N.,Schirmer, T.
      (1998) J.Mol.Biol. 277: 81
    • Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Human Ornithine Aminotransferase
      Shen, B.W.,Ramesh, V.,Mueller, R.,Hohenester, E.,Hennig, M.,Jansonius, J.N.
      (1994) J.Mol.Biol. 243: 128
    • Dl-Canaline and 5-Fluoromethylornithine. Comparison of Two Inactivators of Ornithine Aminotransferase
      Bolkenius, F.N.,Knodgen, B.,Seiler, N.
      (1990) Biochem.J. 268: 409

    Organizational Affiliation

    Division of Structural Biology Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, CH-4056, Switzerland.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A, B, C
439Homo sapiensMutation(s): 0 
Gene Names: OAT
Find proteins for P04181 (Homo sapiens)
Go to Gene View: OAT
Go to UniProtKB:  P04181
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on PFM

Download SDF File 
Download CCD File 
A, B, C
C14 H19 N2 O8 P
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.280α = 90.00
b = 115.280β = 90.00
c = 186.810γ = 120.00
Software Package:
Software NamePurpose
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance