1NJJ

Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray Structure Determination of Trypanosoma brucei Ornithine Decarboxylase Bound to D-Ornithine and to G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL FLEXIBILITY.

Jackson, L.K.Goldsmith, E.J.Phillips, M.A.

(2003) J.Biol.Chem. 278: 22037-22043

  • DOI: 10.1074/jbc.M300188200

  • PubMed Abstract: 
  • Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure o ...

    Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the rate-determining step in the biosynthesis of polyamines. ODC is a proven drug target to treat African sleeping sickness. The x-ray crystal structure of Trypanosoma brucei ODC in complex with d-ornithine (d-Orn), a substrate analog, and G418 (Geneticin), a weak non-competitive inhibitor, was determined to 2.5-A resolution. d-Orn forms a Schiff base with PLP, and the side chain is in a similar position to that observed for putrescine and alpha-difluoromethylornithine in previous T. brucei ODC structures. The d-Orn carboxylate is positioned on the solvent-exposed side of the active site (si face of PLP), and Gly-199, Gly-362, and His-197 are the only residues within 4.2 A of this moiety. This structure confirms predictions that the carboxylate of d-Orn binds on the si face of PLP, and it supports a model in which the carboxyl group of the substrate l-Orn would be buried on the re face of the cofactor in a pocket that includes Phe-397, Tyr-389, Lys-69 (methylene carbons), and Asp-361. Electron density for G418 was observed at the boundary between the two domains within each ODC monomer. A ten-amino acid loop region (392-401) near the 2-fold axis of the dimer interface, which contributes several residues that form the active site, is disordered in this structure. The disordering of residues in the active site provides a potential mechanism for inhibition by G418 and suggests that allosteric inhibition from this site is feasible.


    Organizational Affiliation

    Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, 5323 Harry Hines Boulevard, TX 75390-9041, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ornithine decarboxylase
A, B, C, D
425Trypanosoma brucei gambienseEC: 4.1.1.17
Find proteins for Q9TZZ6 (Trypanosoma brucei gambiense)
Go to UniProtKB:  Q9TZZ6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ORX
Query on ORX

Download SDF File 
Download CCD File 
A, B, C, D
N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
C13 H22 N3 O7 P
OIRLUPUXIUAWOH-LLVKDONJSA-N
 Ligand Interaction
GET
Query on GET

Download SDF File 
Download CCD File 
A, B, C
GENETICIN
G418
C20 H40 N4 O10
BRZYSWJRSDMWLG-DJWUNRQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GETKi: 8000000 nM BINDINGMOAD
ORXKd: 270000 nM BINDINGMOAD
GETKi: 8000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.818α = 90.00
b = 88.540β = 90.03
c = 150.445γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation