2AEX

The 1.58A Crystal Structure of Human Coproporphyrinogen Oxidase Reveals the Structural Basis of Hereditary Coproporphyria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of hereditary coproporphyria.

Lee, D.S.Flachsova, E.Bodnarova, M.Demeler, B.Martasek, P.Raman, C.S.

(2005) Proc.Natl.Acad.Sci.USA 102: 14232-14237

  • DOI: 10.1073/pnas.0506557102

  • PubMed Abstract: 
  • Hereditary coproporphyria is an autosomal dominant disorder resulting from the half-normal activity of coproporphyrinogen oxidase (CPO), a mitochondrial enzyme catalyzing the antepenultimate step in heme biosynthesis. The mechanism by which CPO catal ...

    Hereditary coproporphyria is an autosomal dominant disorder resulting from the half-normal activity of coproporphyrinogen oxidase (CPO), a mitochondrial enzyme catalyzing the antepenultimate step in heme biosynthesis. The mechanism by which CPO catalyzes oxidative decarboxylation, in an extraordinary metal- and cofactor-independent manner, is poorly understood. Here, we report the crystal structure of human CPO at 1.58-A resolution. The structure reveals a previously uncharacterized tertiary topology comprising an unusually flat seven-stranded beta-sheet sandwiched by alpha-helices. In the biologically active dimer (K(D) = 5 x 10(-7) M), one monomer rotates relative to the second by approximately 40 degrees to create an intersubunit interface in close proximity to two independent enzymatic sites. The unexpected finding of citrate at the active site allows us to assign Ser-244, His-258, Asn-260, Arg-262, Asp-282, and Arg-332 as residues mediating substrate recognition and decarboxylation. We favor a mechanism in which oxygen serves as the immediate electron acceptor, and a substrate radical or a carbanion with substantial radical character participates in catalysis. Although several mutations in the CPO gene have been described, the molecular basis for how these alterations diminish enzyme activity is unknown. We show that deletion of residues (392-418) encoded by exon six disrupts dimerization. Conversely, harderoporphyria-causing K404E mutation precludes a type I beta-turn from retaining the substrate for the second decarboxylation cycle. Together, these findings resolve several questions regarding CPO catalysis and provide insights into hereditary coproporphyria.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas Medical School, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coproporphyrinogen III oxidase, mitochondrial
A
346Homo sapiensMutation(s): 0 
Gene Names: CPOX (CPO, CPX)
EC: 1.3.3.3
Find proteins for P36551 (Homo sapiens)
Go to Gene View: CPOX
Go to UniProtKB:  P36551
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • Space Group: P 2 3
  • Diffraction Data DOI: 
    10.15785/SBGRID/85 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 112.741α = 90.00
b = 112.741β = 90.00
c = 112.741γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance