2OAT

ORNITHINE AMINOTRANSFERASE COMPLEXED WITH 5-FLUOROMETHYLORNITHINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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
  • Primary Citation of Related Structures:  
    2OAT

  • PubMed Abstract: 
  • Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC 2.6.1.13), 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 ...

    Ornithine aminotransferase (l-ornithine:2-oxoacid delta-aminotransferase; EC 2.6.1.13), 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ORNITHINE AMINOTRANSFERASEABC439Homo sapiensMutation(s): 0 
Gene Names: OAT
EC: 2.6.1.13
Find proteins for P04181 (Homo sapiens)
Explore P04181 
Go to UniProtKB:  P04181
NIH Common Fund Data Resources
PHAROS  P04181
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PFM
Query on PFM

Download CCD File 
A, B, C
1-AMINO-7-(2-METHYL-3-OXIDO-5-((PHOSPHONOXY)METHYL)-4-PYRIDOXAL-5-OXO-6-HEPTENATE
C14 H19 N2 O8 P
FKVMVCAAQIJMAO-UGEYCXAUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.28α = 90
b = 115.28β = 90
c = 186.81γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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