Yeast coproporphyrinogen oxidase

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Crystal structure of the oxygen-dependent coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae

Phillips, J.D.Whitby, F.G.Warby, C.A.Labbe, P.Yang, C.Pflugrath, J.W.Ferrara, J.D.Robinson, H.Kushner, J.P.Hill, C.P.

(2004) J Biol Chem 279: 38960-38968

  • DOI: https://doi.org/10.1074/jbc.M406050200
  • Primary Citation of Related Structures:  
    1TK1, 1TKL, 1TLB

  • PubMed Abstract: 

    Coproporphyrinogen oxidase (CPO) is an essential enzyme that catalyzes the sixth step of the heme biosynthetic pathway. Unusually for heme biosynthetic enzymes, CPO exists in two evolutionarily and mechanistically distinct families, with eukaryotes and some prokaryotes employing members of the highly conserved oxygen-dependent CPO family. Here, we report the crystal structure of the oxygen-dependent CPO from Saccharomyces cerevisiae (Hem13p), which was determined by optimized sulfur anomalous scattering and refined to a resolution of 2.0 A. The protein adopts a novel structure that is quite different from predicted models and features a central flat seven-stranded anti-parallel sheet that is flanked by helices. The dimeric assembly, which is seen in different crystal forms, is formed by packing of helices and a short isolated strand that forms a beta-ladder with its counterpart in the partner subunit. The deep active-site cleft is lined by conserved residues and has been captured in open and closed conformations in two different crystal forms. A substratesized cavity is completely buried in the closed conformation by the approximately 8-A movement of a helix that forms a lid over the active site. The structure therefore suggests residues that likely play critical roles in catalysis and explains the deleterious effect of many of the mutations associated with the disease hereditary coproporphyria.

  • Organizational Affiliation

    Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coproporphyrinogen III oxidase326Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: HEM13YDR044WYD5112.02
Find proteins for P11353 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11353 
Go to UniProtKB:  P11353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11353
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 232.773α = 90
b = 65.238β = 107.85
c = 166.071γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance