Human Pyridoxine-5'-phosphate oxidase in complex with PLP

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Identification of the pyridoxal 5'-phosphate allosteric site in human pyridox(am)ine 5'-phosphate oxidase.

Barile, A.Graziani, C.Antonelli, L.Parroni, A.Fiorillo, A.di Salvo, M.L.Ilari, A.Giorgi, A.Rosignoli, S.Paiardini, A.Contestabile, R.Tramonti, A.

(2024) Protein Sci 33: e4900-e4900

  • DOI: https://doi.org/10.1002/pro.4900
  • Primary Citation of Related Structures:  
    8QYT, 8QYW

  • PubMed Abstract: 

    Adequate levels of pyridoxal 5'-phosphate (PLP), the catalytically active form of vitamin B 6 , and its proper distribution in the body are essential for human health. The PLP recycling pathway plays a crucial role in these processes and its defects cause severe neurological diseases. The enzyme pyridox(am)ine 5'-phosphate oxidase (PNPO), whose catalytic action yields PLP, is one of the key players in this pathway. Mutations in the gene encoding PNPO are responsible for a severe form of neonatal epilepsy. Recently, PNPO has also been described as a potential target for chemotherapeutic agents. Our laboratory has highlighted the crucial role of PNPO in the regulation of PLP levels in the cell, which occurs via a feedback inhibition mechanism of the enzyme, exerted by binding of PLP at an allosteric site. Through docking analyses and site-directed mutagenesis experiments, here we identified the allosteric PLP binding site of human PNPO. This site is located in the same protein region as the allosteric site we previously identified in the Escherichia coli enzyme homologue. However, the identity and arrangement of the amino acid residues involved in PLP binding are completely different and resemble those of the active site of PLP-dependent enzymes. The identification of the PLP allosteric site of human PNPO paves the way for the rational design of enzyme inhibitors as potential anti-cancer compounds.

  • Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxine-5'-phosphate oxidase264Homo sapiensMutation(s): 0 
Gene Names: PNPO
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVS9 (Homo sapiens)
Explore Q9NVS9 
Go to UniProtKB:  Q9NVS9
GTEx:  ENSG00000108439 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVS9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.48α = 90
b = 82.48β = 90
c = 59.19γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release