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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9FXQ

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 55.34 kDa 
  • Atom Count: 3,729 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 482 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CPS
(Subject of Investigation/LOI)

Query on CPS



Download:Ideal Coordinates CCD File
B [auth A]3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N

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

View Full Validation Report



Ligand Structure Quality Assessment 


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