Coproporphyrinogen III oxidase (HemN) from Escherichia coli is a Radical SAM enzyme.

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Crystal Structure of Coproporphyrinogen III Oxidase Reveals Cofactor Geometry of Radical Sam Enzymes

Layer, G.Moser, J.Heinz, D.W.Jahn, D.Schubert, W.-D.

(2003) EMBO J 22: 6214

  • DOI: https://doi.org/10.1093/emboj/cdg598
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    'Radical SAM' enzymes generate catalytic radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. We present the first crystal structure of a Radical SAM enzyme, that of HemN, the Escherichia coli oxygen-independent coproporphyrinogen III oxidase, at 2.07 A resolution. HemN catalyzes the essential conversion of coproporphyrinogen III to protoporphyrinogen IX during heme biosynthesis. HemN binds a 4Fe-4S cluster through three cysteine residues conserved in all Radical SAM enzymes. A juxtaposed SAM coordinates the fourth Fe ion through its amide nitrogen and carboxylate oxygen. The SAM sulfonium sulfur is near both the Fe (3.5 A) and a neighboring sulfur of the cluster (3.6 A), allowing single electron transfer from the 4Fe-4S cluster to the SAM sulfonium. SAM is cleaved yielding a highly oxidizing 5'-deoxyadenosyl radical. HemN, strikingly, binds a second SAM immediately adjacent to the first. It may thus successively catalyze two propionate decarboxylations. The structure of HemN reveals the cofactor geometry required for Radical SAM catalysis and sets the stage for the development of inhibitors with antibacterial function due to the uniquely bacterial occurrence of the enzyme.

  • Organizational Affiliation

    Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EC: 1.3
Find proteins for P32131 (Escherichia coli (strain K12))
Explore P32131 
Go to UniProtKB:  P32131
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32131
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.036α = 90
b = 114.036β = 90
c = 76.459γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other