Ferredoxin:CoB-CoM heterodisulfide reductase

 

Methyl-coenzyme M (methyl-S-CoM) and coenzyme B (HS-CoB) form the heterodisulfide CoM-S-S-CoB which can be reduced back to HS-CoB and HS-CoM by the HdrABC enzyme complex.

The reaction takes place in the HdrB subunit of the HdrABC-MvhAGD complex, which is of interest because it catalyses an iron-sulfur cluster-assisted disulfide reduction mechanism. HdrB adopts an aspartate racemase-like fold with two similar noncubane [4Fe-4S] clusters composed of highly distorted [3Fe-3S] and [2Fe-2S] subclusters. The subunit contains a duplicated CCG motif which is predicted to be a binding motif for iron-sulfur clusters.

 

Reference Protein and Structure

Sequence
A0A2D0TCB4 UniProt IPR039650, IPR017678 (Sequence Homologues) (PDB Homologues)
Biological species
Methanothermococcus thermolithotrophicus DSM 2095 Uniprot
PDB
5odi - Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH (2.4 Å) PDBe PDBsum 5odi
Catalytic CATH Domains
(see all for 5odi)
Cofactors
Non-cubane [4fe-4s]-cluster (2), Tetra-mu3-sulfido-tetrairon (1), Fadh2(2-) (2)
Click To Show Structure

Enzyme Reaction (EC:1.8.7.3)

hydron
CHEBI:15378ChEBI
+
CoM-S-S-CoB(4-)
CHEBI:58411ChEBI
+
di-mu-sulfido-diiron(1+)
CHEBI:33738ChEBI
→
coenzyme M(1-)
CHEBI:58319ChEBI
+
coenzyme B(3-)
CHEBI:58596ChEBI
+
di-mu-sulfido-diiron(2+)
CHEBI:33737ChEBI
Alternative enzyme names: HdrABC (gene names), HdrA1B1C1 (gene names), HdrA2B2C2 (gene names),

Enzyme Mechanism

Introduction

This mechanism involves clamping of the CoM-S-S-CoB heterodisulfide between the two exposed iron atoms of the noncubane [4Fe-4S] clusters. The heterodisulfide is homolytically cleaved leaving coenzyme M and B bound to the noncubane clusters, forming pentavalent Fe-S species. The [4Fe-4S]-S-CoB adduct is reduced, releasing HS-CoB. Electron transfer to [4Fe-4S]-S-CoM then results in dissociation of HS-CoM. Delivery of a single electron to the reductase site may be supplied from H2 via FAD.

Catalytic Residues Roles

UniProt PDB* (5odi)
Cys153, Cys193, Cys194, Cys234, Cys231, Cys41, Cys42, Cys9, Cys78, Cys81 Cys153B, Cys193B, Cys194B, Cys234B, Cys231B, Cys41B, Cys42B, Cys9B, Cys78B, Cys81B Cysteine ligands coordinated to Fe of noncubane iron sulfur clusters. metal ligand
His154 His154B His154 in direct contact with coenzyme M, a possible route for protons to reach the active site. proton donor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

enzyme-substrate complex formation, intermediate formation, overall reactant used, homolysis, cofactor used, proton transfer, electron transfer, enzyme-substrate complex cleavage, overall product formed

References

  1. Wagner T et al. (2017), Science, 357, 699-703. Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. DOI:10.1126/science.aan0425. PMID:28818947.
  2. Kumar AK et al. (2015), Biochemistry, 54, 3122-3128. Structural and Biochemical Characterization of a Ferredoxin:Thioredoxin Reductase-like Enzyme from Methanosarcina acetivorans. DOI:10.1021/acs.biochem.5b00137. PMID:25915695.

Step 1. The disulfide bridge of CoM-S-S-CoB clamps between the two exposed iron atoms of the noncubane [4Fe-4S] clusters.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys153B metal ligand
Cys193B metal ligand
Cys194B metal ligand
Cys234B metal ligand
Cys231B metal ligand
Cys41B metal ligand
Cys42B metal ligand
Cys9B metal ligand
Cys78B metal ligand
Cys81B metal ligand

Chemical Components

enzyme-substrate complex formation

Step 2. CoM-S-S-CoB is homolytically cleaved, leaving the coenzyme M and B sulfurs bound to the Fe-S clusters which thereby become oxidised. Pentavalent Fe-S species form.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys153B metal ligand
Cys193B metal ligand
Cys194B metal ligand
Cys234B metal ligand
Cys231B metal ligand
Cys41B metal ligand
Cys42B metal ligand
Cys9B metal ligand
Cys78B metal ligand
Cys81B metal ligand

Chemical Components

intermediate formation, overall reactant used, homolysis, cofactor used

Step 3. The [4Fe-4S]-S-CoB adduct is reduced and HS-CoB is released.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys153B metal ligand
Cys193B metal ligand
Cys194B metal ligand
Cys234B metal ligand
Cys231B metal ligand
Cys41B metal ligand
Cys42B metal ligand
Cys9B metal ligand
Cys78B metal ligand
Cys81B metal ligand

Chemical Components

proton transfer, electron transfer, enzyme-substrate complex cleavage, overall product formed, cofactor used

Step 4. Electron transfer to [4Fe-4S]-S-CoM results in dissociation of HS-CoM. CoM is in direct contact with His154 which may be a means for proton transfer and must be protonated from bulk solvent prior to this step (not shown).

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His154B proton donor
Cys153B metal ligand
Cys193B metal ligand
Cys194B metal ligand
Cys234B metal ligand
Cys231B metal ligand
Cys41B metal ligand
Cys42B metal ligand
Cys9B metal ligand
Cys78B metal ligand
Cys81B metal ligand

Chemical Components

proton transfer, electron transfer, enzyme-substrate complex cleavage, overall product formed, cofactor used
Download: Image, Marvin File

Step 1. The disulfide bridge of CoM-S-S-CoB clamps between the two exposed iron atoms of the noncubane [4Fe-4S] clusters.

Step 2. CoM-S-S-CoB is homolytically cleaved, leaving the coenzyme M and B sulfurs bound to the Fe-S clusters which thereby become oxidised. Pentavalent Fe-S species form.

Step 3. The [4Fe-4S]-S-CoB adduct is reduced and HS-CoB is released.

Step 4. Electron transfer to [4Fe-4S]-S-CoM results in dissociation of HS-CoM. CoM is in direct contact with His154 which may be a means for proton transfer and must be protonated from bulk solvent prior to this step (not shown).

Products.

Contributors

Noa Marson, Antonio Ribeiro