Structure of an intellectual disability-associated ornithine decarboxylase variant G84R

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R.

Zhou, X.E.Schultz, C.R.Suino Powell, K.Henrickson, A.Lamp, J.Brunzelle, J.S.Demeler, B.Vega, I.E.Bachmann, A.S.Melcher, K.

(2022) ACS Omega 7: 34665-34675

  • DOI: https://doi.org/10.1021/acsomega.2c04702
  • Primary Citation of Related Structures:  
    7U6P, 7U6U

  • PubMed Abstract: 

    Ornithine decarboxylase (ODC) is a rate-limiting enzyme for the synthesis of polyamines (PAs). PAs are required for proliferation, and increased ODC activity is associated with cancer and neural over-proliferation. ODC levels and activity are therefore tightly regulated, including through the ODC-specific inhibitor, antizyme AZ1. Recently, ODC G84R has been reported as a partial loss-of-function variant that is associated with intellectual disability and seizures. However, G84 is distant from both the catalytic center and the ODC homodimerization interface. To understand how G84R modulates ODC activity, we have determined the crystal structure of ODC G84R in both the presence and the absence of the cofactor pyridoxal 5-phosphate. The structures show that the replacement of G84 by arginine leads to hydrogen bond formation of R84 with F420, the last residue of the ODC C-terminal helix, a structural element that is involved in the AZ1-mediated proteasomal degradation of ODC. In contrast, the catalytic center is essentially indistinguishable from that of wildtype ODC. We therefore reanalyzed the catalytic activity of ODC G84R and found that it is rescued when the protein is purified in the presence of a reducing agent to mimic the reducing environment of the cytoplasm. This suggests that R84 may exert its neurological effects not through reducing ODC catalytic activity but through misregulation of its AZ1-mediated proteasomal degradation.

  • Organizational Affiliation

    Northwestern University Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ornithine decarboxylase
A, B
424Homo sapiensMutation(s): 1 
Gene Names: ODC1
UniProt & NIH Common Fund Data Resources
Find proteins for P11926 (Homo sapiens)
Explore P11926 
Go to UniProtKB:  P11926
PHAROS:  P11926
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11926
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.806α = 90
b = 85.879β = 90
c = 154.738γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
pointlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM120600
Canada Research ChairsCanadaC150-2017-00015
Canada Foundation for InnovationCanadaCFI-37589

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description