PDBsum entry: 1olt

Oxidoreductase

PDB id: 1olt

Contents

Protein chain

434 a.a. *

Ligands

SF4-SAM

SAM

Waters ×396

* Residue conservation analysis

PDB id:

1olt

Name:

Oxidoreductase

Title:

Coproporphyrinogen iii oxidase (hemn) from escherichia coli is a radical sam enzyme.

Structure:

Oxygen-independent coproporphyrinogen iii oxidase chain: a. Synonym: coproporphyrinogenase, coprogen oxidase. Ec: 1.3.-.-

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12

Resolution:

2.07Å R-factor: 0.155 R-free: 0.187

Authors:

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

Key ref:

G.Layer et al. (2003). Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes. EMBO J, 22, 6214-6224. PubMed id: 14633981 DOI: 10.1093/emboj/cdg598

Date:

13-Aug-03 Release date: 04-Dec-03

Protein chain

P32131  (HEMN_ECOLI) -  Oxygen-independent coproporphyrinogen-III oxidase

Seq: 457 a.a.

Struc: 434 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.3.99.22 - Coproporphyrinogen dehydrogenase.
• Pathway: Porphyrin Biosynthesis (later stages)
• Reaction: Coproporphyrinogen-III + 2 S-adenosyl-L-methionine = protoporphyrinogen- IX + 2 CO₂ + 2 L-methionine + 2 5'-deoxyadenosine

Coproporphyrinogen-III + 2 × S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = protoporphyrinogen- IX + 2 × CO(2) + 2 × L-methionine + 2 × 5'-deoxyadenosine

• Cofactor: Iron-sulfur

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1093/emboj/cdg598

EMBO J 22:6214-6224 (2003)

PubMed id: 14633981

Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes.

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

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.

Selected figure(s)

Figure 1.
Figure 1 Schematic representation of the enzymatic reaction of HemN. (A) HemN oxidatively decarboxylates coproporphyrinogen III to protoporphyrinogen IX by converting the propionate side chains of rings A and B to the corresponding vinyl groups. (B) The first reaction step common to HemN and all Radical SAM enzymes: a reduced 4Fe -4S cluster transfers an electron to the sulfonium of S-adenosylmethionine (SAM). The C5' -S+ bond of SAM is cleaved, producing methionine and a highly oxidizing 5'-deoxyadenosyl radical. The radical abstracts a hydrogen atom from a substrate RH (the substrate may itself be an enzyme), creating the corresponding substrate radical (R ). (C) In the reaction catalyzed by HemN, the 5'-deoxyadenosyl radical abstracts a hydrogen atom from the -C atom of the substrate propionate side chain. CO[2] is eliminated, and a single electron transfer to an electron acceptor gives rise to the vinyl group of the reaction product.

Figure 2.
Figure 2 Structure of HemN. (A) A ribbons-type and (B) a schematic representation of the secondary structure elements. HemN consists of two distinct domains (shades of blue and red) as well as an elongated N-terminal region termed a trip-wire (green). The catalytic domain is built around a 12-stranded, largely parallel -sheet. At its core, the N-terminal region bears a three-quarter barrel, a ( )[6] variation of the ( )[8] TIM barrel. This core binds all cofactors, a 4Fe -4S cluster and two SAM molecules. The N-terminal trip-wire and the C-terminal domain probably participate in substrate binding. A CxxxCxxC motif, conserved in all Radical SAM proteins, is located in a loop following the first -strand of the central barrel. The three cysteines (small yellow circles) bind three of the Fe ions of the cluster.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 6214-6224) copyright 2003.

Figures were selected by the author.

Author's comment

A common step in the biosynthesis of hemes and chlorophylls involves the oxidative decarboxylation of coproporphyrinogen III to protoporphyrinogen IX.
This requires the conversion of the propionate side chains of rings A and B to the corresponding vinyl groups. The reaction is catalyzed by two mechanistically unrelated coproporphyrinogen III oxidases (CPOs): In the presence of oxygen, oxygen-dependent HemF catalyzes the reaction. Under anaerobic conditions HemN takes over. HemN is not only oxygen-independent but is also highly sensitive towards oxygen.
Mechanistically and structurally HemN is a member of the "Radical SAM" family of enzymes. These enzymes all contain a conserved motif consisting of three cysteins that bind a [4Fe-4S] cluster. The fourth iron of the cluster is coordinated by S-adenosylmethionine (SAM). Reduction of the [4Fe-4S] cluster transfers an electron to SAM homolytically cleaving it to methionine and a 5'-deoxyadenosyl radical. The latter abstracts a hydrogen atom (proton plus electron) from a substrate resulting in a substrate-based radical, which allows potentially difficult rearrangement reactions. Finally, the unpaired electron is either transferred to a terminal electron acceptor, as in HemN, or transferred back to regenerate the 5'-adenosyl radical.
The structures of three Radical SAM enzymes, HemN, Biotin synthase (BioB) and MoaA (first enzyme in Mo-cofactor synthesis) were published in quick succession. They confirm the involvement of SAM in [4Fe-4S] cluster coordination, proposed previously. They also indicate that Radical SAM enzymes structurally derive from the beta-barrel fold.
Wolf-Dieter Schubert