5BWA

Crystal structure of ODC-PLP-AZ1 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of Ornithine Decarboxylase inactivation and accelerated degradation by polyamine sensor Antizyme1

Wu, D.H.Kaan, H.Y.Zheng, X.Tang, X.He, Y.Vanessa Tan, Q.Zhang, N.Song, H.

(2015) Sci Rep 5: 14738-14738

  • DOI: 10.1038/srep14738

  • PubMed Abstract: 
  • Ornithine decarboxylase (ODC) catalyzes the first and rate-limiting step of polyamine biosynthesis in humans. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. Excessi ...

    Ornithine decarboxylase (ODC) catalyzes the first and rate-limiting step of polyamine biosynthesis in humans. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. Excessive accumulation of polyamines has a cytotoxic effect on cells and elevated level of ODC activity is associated with cancer development. To maintain normal cellular proliferation, regulation of polyamine synthesis is imposed by Antizyme1 (AZ1). The expression of AZ1 is induced by a ribosomal frameshifting mechanism in response to increased intracellular polyamines. AZ1 regulates polyamine homeostasis by inactivating ODC activity and enhancing its degradation. Here, we report the structure of human ODC in complex with N-terminally truncated AZ1 (cAZ1). The structure shows cAZ1 binding to ODC, which occludes the binding of a second molecule of ODC to form the active homodimer. Consequently, the substrate binding site is disrupted and ODC is inactivated. Structural comparison shows that the binding of cAZ1 to ODC causes a global conformational change of ODC and renders its C-terminal region flexible, therefore exposing this region for degradation by the 26S proteasome. Our structure provides the molecular basis for the inactivation of ODC by AZ1 and sheds light on how AZ1 promotes its degradation.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ornithine decarboxylase
A
461Homo sapiensMutation(s): 0 
Gene Names: ODC1
EC: 4.1.1.17
Find proteins for P11926 (Homo sapiens)
Go to Gene View: ODC1
Go to UniProtKB:  P11926
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ornithine decarboxylase antizyme 1
B
160Homo sapiensMutation(s): 0 
Gene Names: OAZ1 (OAZ)
Find proteins for P54368 (Homo sapiens)
Go to Gene View: OAZ1
Go to UniProtKB:  P54368
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
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: 3.2 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.154α = 90.00
b = 74.084β = 90.00
c = 157.083γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-07 
  • Released Date: 2015-12-09 
  • Deposition Author(s): Wu, D.H.

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release