9FXQ | pdb_00009fxq

Ancestral Prenylcysteine Oxidase 1 (PCYOX1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.275 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Evolution, structure, and drug-metabolizing activity of mammalian prenylcysteine oxidases.

Barone, M.Pizzorni, L.Fraaije, M.W.Mascotti, M.L.Mattevi, A.

(2024) J Biological Chem 300: 107810-107810

  • DOI: https://doi.org/10.1016/j.jbc.2024.107810
  • Primary Citation of Related Structures:  
    9FXQ

  • PubMed Abstract: 

    Prenylcysteine oxidases (PCYOXs) metabolize prenylated cysteines produced by protein degradation. They utilize oxygen as co-substrate to produce free cysteine, an aldehyde, and hydrogen peroxide through the unusual oxidation of a thioether bond. In this study, we explore the evolution, structure, and mechanism of the two mammalian PCYOXs. A gene duplication event in jawed vertebrates originated these two paralogs. Both enzymes are active on farnesyl- and geranylgeranylcysteine, but inactive on molecules with shorter prenyl groups. Kinetics experiments outline a mechanism where flavin reduction and re-oxidation occur rapidly without any detectable intermediates, with the overall reaction rate limited by product release. The experimentally determined three-dimensional structure of PCYOX1 reveals long and wide tunnels leading from the surface to the flavin. They allow the isoprene substrate to curl up within the protein and position its reactive cysteine group close to the flavin. A hydrophobic patch on the surface mediates membrane association, enabling direct substrate and product exchange with the lipid bilayer. Leveraging established knowledge on flavoenzyme inhibition, we designed sub-micromolar PCYOX inhibitors. Additionally, we discovered that PCYOXs bind and slowly degrade salisirab, an anti-RAS compound. This activity suggests potential and previously unknown roles of PCYOXs in drug metabolism.


  • Organizational Affiliation
    • Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy 27100.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ancestral Prenylcysteine Oxidase 1 (PCYOX1)482MammaliaMutation(s): 0 
EC: 1.8.3.5
UniProt
Find proteins for A0A7N4P0D0 (Sarcophilus harrisii)
Explore A0A7N4P0D0 
Go to UniProtKB:  A0A7N4P0D0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7N4P0D0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.275 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.659α = 90
b = 172.659β = 90
c = 172.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly2020CW39SJ

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references