2BYJ

Ornithine aminotransferase mutant Y85I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Determinants of Substrate Specificity in Omega-Aminotransferases.

Markova, M.Peneff, C.Hewlins, M.J.E.Schirmer, T.John, R.A.

(2005) J.Biol.Chem. 280: 36409

  • DOI: 10.1074/jbc.M506977200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ornithine aminotransferase and 4-aminobutyrate aminotransferase are related pyridoxal phosphate-dependent enzymes having different substrate specificities. The atomic structures of these enzymes have shown (i) that active site differences are limited ...

    Ornithine aminotransferase and 4-aminobutyrate aminotransferase are related pyridoxal phosphate-dependent enzymes having different substrate specificities. The atomic structures of these enzymes have shown (i) that active site differences are limited to the steric positions occupied by two tyrosine residues in ornithine aminotransferase and (ii) that, uniquely among related, structurally characterized aminotransferases, the conserved arginine that binds the alpha-carboxylate of alpha-amino acids interacts tightly with a glutamate residue. To determine the contribution of these residues to the specificities of the enzymes, we analyzed site-directed mutants of ornithine aminotransferase by rapid reaction kinetics, x-ray crystallography, and 13C NMR spectroscopy. Mutation of one tyrosine (Tyr-85) to isoleucine, as found in aminobutyrate aminotransferase, decreased the rate of the reaction of the enzyme with ornithine 1000-fold and increased that with 4-aminobutyrate 16-fold, indicating that Tyr-85 is a major determinant of specificity toward ornithine. Unexpectedly, the limiting rate of the second half of the reaction, conversion of ketoglutarate to glutamate, was greatly increased, although the kinetics of the reverse reaction were unaffected. A mutant in which the glutamate (Glu-235) that interacts with the conserved arginine was replaced by alanine retained its regiospecificity for the delta-amino group of ornithine, but the glutamate reaction was enhanced 650-fold, whereas only a 5-fold enhancement of the ketoglutarate reaction rate resulted. A model is proposed in which conversion of the enzyme to its pyridoxamine phosphate form disrupts the internal glutamate-arginine interaction, thus enabling ketoglutarate but not glutamate to be a good substrate.


    Organizational Affiliation

    School of Biosciences and School of Chemistry, Cardiff University, P. O. Box 911, CF23 6QU, Wales, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORNITHINE AMINOTRANSFERASE
A, B, C
439Homo sapiensMutations: I85Y
Gene Names: OAT
EC: 2.6.1.13
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
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.02 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.723α = 90.00
b = 115.723β = 90.00
c = 186.551γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-07
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-04-04
    Type: Data collection