4ZGY

STRUCTURE of HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 

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This is version 1.2 of the entry. See complete history


Literature

Structural basis of antizyme-mediated regulation of polyamine homeostasis

Wu, H.Y.Chen, S.F.Hsieh, J.Y.Chou, F.Wang, Y.H.Lin, W.T.Lee, P.Y.Yu, Y.J.Lin, L.Y.Lin, T.S.Lin, C.L.Liu, G.Y.Tzeng, S.R.Hung, H.C.Chan, N.L.

(2015) Proc Natl Acad Sci U S A 112: 11229-11234

  • DOI: 10.1073/pnas.1508187112
  • Primary Citation of Related Structures:  
    4ZGY, 4ZGZ

  • PubMed Abstract: 
  • Polyamines are organic polycations essential for cell growth and differentiation; their aberrant accumulation is often associated with diseases, including many types of cancer. To maintain polyamine homeostasis, the catalytic activity and protein abundance of ornithine decarboxylase (ODC), the committed enzyme for polyamine biosynthesis, are reciprocally controlled by the regulatory proteins antizyme isoform 1 (Az1) and antizyme inhibitor (AzIN) ...

    Polyamines are organic polycations essential for cell growth and differentiation; their aberrant accumulation is often associated with diseases, including many types of cancer. To maintain polyamine homeostasis, the catalytic activity and protein abundance of ornithine decarboxylase (ODC), the committed enzyme for polyamine biosynthesis, are reciprocally controlled by the regulatory proteins antizyme isoform 1 (Az1) and antizyme inhibitor (AzIN). Az1 suppresses polyamine production by inhibiting the assembly of the functional ODC homodimer and, most uniquely, by targeting ODC for ubiquitin-independent proteolytic destruction by the 26S proteasome. In contrast, AzIN positively regulates polyamine levels by competing with ODC for Az1 binding. The structural basis of the Az1-mediated regulation of polyamine homeostasis has remained elusive. Here we report crystal structures of human Az1 complexed with either ODC or AzIN. Structural analysis revealed that Az1 sterically blocks ODC homodimerization. Moreover, Az1 binding triggers ODC degradation by inducing the exposure of a cryptic proteasome-interacting surface of ODC, which illustrates how a substrate protein may be primed upon association with Az1 for ubiquitin-independent proteasome recognition. Dynamic and functional analyses further indicated that the Az1-induced binding and degradation of ODC by proteasome can be decoupled, with the intrinsically disordered C-terminal tail fragment of ODC being required only for degradation but not binding. Finally, the AzIN-Az1 structure suggests how AzIN may effectively compete with ODC for Az1 to restore polyamine production. Taken together, our findings offer structural insights into the Az-mediated regulation of polyamine homeostasis and proteasomal degradation.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan; Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan; nlchan@ntu.edu.tw srtzeng@ntu.edu.tw hchung@dragon.nchu.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ornithine decarboxylaseA422Homo 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 1B135Homo 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 2 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
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.698α = 90
b = 73.368β = 90
c = 162.084γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKLdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-04-24 
  • Released Date: 2015-09-02 
  • Deposition Author(s): Wu, H.Y., Chan, N.L.

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwanNSC99-2113-M-002-008-MY3
Ministry of Science and TechnologyTaiwanNSC101-2911-I-002-303-
National Research Program for BiopharmaceuticalsTaiwanNSC101-2325-B-002-049
National Taiwan UniversityTaiwanNTU-102-027-MY3
National Taiwan UniversityTaiwanNTU-103-008-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Database references