4IVM

Structure of human protoporphyrinogen IX oxidase(R59G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

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This is version 1.2 of the entry. See complete history


Literature

Quantitative structural insight into human variegate porphyria disease.

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

(2013) J Biol Chem 288: 11731-11740

  • DOI: https://doi.org/10.1074/jbc.M113.459768
  • Primary Citation of Related Structures:  
    4IVM, 4IVO

  • PubMed Abstract: 

    Defects in the human protoporphyrinogen oxidase (hPPO) gene, resulting in ~50% decreased activity of hPPO, is responsible for the dominantly inherited disorder variegate porphyria (VP). To understand the molecular mechanism of VP, we employed the site-directed mutagenesis, biochemical assays, structural biology, and molecular dynamics simulation studies to investigate VP-causing hPPO mutants. We report here the crystal structures of R59Q and R59G mutants in complex with acifluorfen at a resolution of 2.6 and 2.8 Å. The r.m.s.d. of the Cα atoms of the active site structure of R59G and R59Q with respect to the wild-type was 0.20 and 0.15 Å, respectively. However, these highly similar static crystal structures of mutants with the wild-type could not quantitatively explain the observed large differences in their enzymatic activity. To understand how the hPPO mutations affect their catalytic activities, we combined molecular dynamics simulation and statistical analysis to quantitatively understand the molecular mechanism of VP-causing mutants. We have found that the probability of the privileged conformations of hPPO can be correlated very well with the k(cat)/K(m) of PPO (correlation coefficient, R(2) > 0.9), and the catalytic activity of 44 clinically reported VP-causing mutants can be accurately predicted. These results indicated that the VP-causing mutation affect the catalytic activity of hPPO by affecting the ability of hPPO to sample the privileged conformations. The current work, together with our previous crystal structure study on the wild-type hPPO, provided the quantitative structural insight into human variegate porphyria disease.


  • Organizational Affiliation

    State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry, Nankai University, Tianjin 300071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protoporphyrinogen oxidaseA [auth B]483Homo sapiensMutation(s): 1 
Gene Names: PPOX
EC: 1.3.3.4
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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ACJ BindingDB:  4IVM Ki: 1710 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.098α = 90
b = 136.098β = 90
c = 158.361γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations