Structure of human protoporphyrinogen IX oxidase

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural insight into human variegate porphyria disease

Qin, X.Tan, Y.Wang, L.Wang, Z.Wang, B.Wen, X.Yang, G.Xi, Z.Shen, Y.

(2011) FASEB J 25: 653-664

  • DOI: https://doi.org/10.1096/fj.10-170811
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human protoporphyrinogen IX oxidase (hPPO), a mitochondrial inner membrane protein, converts protoporphyrinogen IX to protoporphyrin IX in the heme biosynthetic pathway. Mutations in the hPPO gene cause the inherited human disease variegate porphyria (VP). In this study, we report the crystal structure of hPPO in complex with the coenzyme flavin adenine dinucleotide (FAD) and the inhibitor acifluorfen at a resolution of 1.9 Å. The structural and biochemical analyses revealed the molecular details of FAD and acifluorfen binding to hPPO as well as the interactions of the substrate with hPPO. Structural analysis and gel chromatography indicated that hPPO is a monomer rather than a homodimer in vitro. The founder-effect mutation R59W in VP patients is most likely caused by a severe electrostatic hindrance in the hydrophilic binding pocket involving the bulky, hydrophobic indolyl ring of the tryptophan. Forty-seven VP-causing mutations were purified by chromatography and kinetically characterized in vitro. The effect of each mutation was demonstrated in the high-resolution crystal structure.

  • Organizational Affiliation

    College of Life Science, Nankai University, Tianjin, China 300071.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protoporphyrinogen oxidase477Homo sapiensMutation(s): 0 
Gene Names: PPOX
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P50336 (Homo sapiens)
Explore P50336 
Go to UniProtKB:  P50336
PHAROS:  P50336
GTEx:  ENSG00000143224 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50336
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ACJ BindingDB:  3NKS Ki: 1710 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.702α = 90
b = 136.702β = 90
c = 158.877γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2011-04-20 
  • Deposition Author(s): Shen, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description