1OLT

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

Summary for 1OLT

• Entry DOI: 10.2210/pdb1olt/pdb
• Descriptor: OXYGEN-INDEPENDENT COPROPORPHYRINOGEN III OXIDASE, IRON/SULFUR CLUSTER, S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: heme biosynthesis, decarboxylase, radical sam enzyme, 4fe- 4s cluster, s-adenosyl-l-methionine, oxidoreductase
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 53930.34

Authors

Layer, G.,Moser, J.,Heinz, D.W.,Jahn, D.,Schubert, W.-D. (deposition date: 2003-08-13, release date: 2003-12-04, Last modification date: 2024-05-08)

Primary citation

Layer, G.,Moser, J.,Heinz, D.W.,Jahn, D.,Schubert, W.-D.
Crystal Structure of Coproporphyrinogen III Oxidase Reveals Cofactor Geometry of Radical Sam Enzymes
Embo J., 22:6214-, 2003

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.

PubMed: 14633981
DOI: 10.1093/EMBOJ/CDG598

Experimental method

X-RAY DIFFRACTION (2.07 Å)