5BWA

Crystal structure of ODC-PLP-AZ1 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

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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
  • Primary Citation of Related Structures:  
    5BWA

  • 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. Excessive accumulation of polyamines has a cytotoxic effect on cells and elevated level of ODC activity is associated with cancer development ...

    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

    Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ornithine decarboxylaseA461Homo sapiensMutation(s): 0 
Gene Names: ODC1
EC: 4.1.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P11926 (Homo sapiens)
Explore P11926 
Go to UniProtKB:  P11926
PHAROS:  P11926
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ornithine decarboxylase antizyme 1B160Homo sapiensMutation(s): 0 
Gene Names: OAZ1OAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P54368 (Homo sapiens)
Explore P54368 
Go to UniProtKB:  P54368
PHAROS:  P54368
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.154α = 90
b = 74.084β = 90
c = 157.083γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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