Secondary-alcohol dehydrogenase (coenzyme-F420)

 

F420-dependent secondary alcohol dehydrogenase (Adf) from Methanoculleus thermophillicus is a member of the bacterial luciferase family. It catalyses the reduction of secondary alcohols no larger than isopentanol into their corresponding ketones, and is involved in the final process of anaerobic degradation of biomass.

 

Reference Protein and Structure

Sequence
O93734 UniProt IPR019945 (Sequence Homologues) (PDB Homologues)
Biological species
Methanoculleus thermophilus (Archaea) Uniprot
PDB
1rhc - F420-dependent secondary alcohol dehydrogenase in complex with an F420-acetone adduct (1.8 Å) PDBe PDBsum 1rhc
Catalytic CATH Domains
3.20.20.30 CATHdb (see all for 1rhc)
Click To Show Structure

Enzyme Reaction (EC:1.1.98.5)

secondary alcohol
CHEBI:35681ChEBI
+
hydron
CHEBI:15378ChEBI
+
coenzyme gamma-F420-2(5-)
CHEBI:57922ChEBI
→
ketone
CHEBI:17087ChEBI
+
1,5-dihydrocoenzyme F420(4-)
CHEBI:57530ChEBI
Alternative enzyme names: F420-dependent alcohol dehydrogenase, Secondary alcohol:F420 oxidoreductase, F420-dependent secondary alcohol dehydrogenase,

Enzyme Mechanism

Introduction

His 39 deprotonates the hydroxyl group of the alcohol substrate, resulting in a hydride transfer from the substrate C2 onto F420 C5 atom. The alcoholate anion transition state is stabilised by hydrogen bonding to Trp 43 and protonated Glu 108. N10 of F420 is protonated by Glu 108.

Catalytic Residues Roles

UniProt PDB* (1rhc)
Glu108 Glu108A Protonated Glu 108 helps to stabilise the partially formed alcoholate anion. Glu 108 then protonates the N10 atom of F420. proton acceptor, electrostatic stabiliser, proton donor
His39 His39A His 39 acts as a general base by deprotonating the hydroxyl of the alcohol. proton acceptor, proton donor
Trp43 Trp43A Stabilises the partially formed alcoholate anion. electrostatic stabiliser
*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

proton transfer, hydride transfer, bimolecular nucleophilic addition, cofactor used, native state of cofactor is not regenerated, overall product formed, inferred reaction step

References

  1. Aufhammer SW et al. (2004), Structure, 12, 361-370. Coenzyme Binding in F420-Dependent Secondary Alcohol Dehydrogenase, a Member of the Bacterial Luciferase Family. DOI:10.1016/j.str.2004.02.010. PMID:15016352.

Step 1. His39 deprotonates the hydroxyl group of the substrate. A hydride is transferred from the C2 of the substrate to C5 of F420. The oxidised product is formed.

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Catalytic Residues Roles

Residue Roles
Trp43A electrostatic stabiliser
Glu108A electrostatic stabiliser
His39A proton acceptor

Chemical Components

proton transfer, hydride transfer, ingold: bimolecular nucleophilic addition, cofactor used, native state of cofactor is not regenerated, overall product formed

Step 2. Glu108 protonates N10 of the reduced F420 cofactor.

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Catalytic Residues Roles

Residue Roles
Glu108A proton donor

Chemical Components

proton transfer

Step 3. In an inferred step His39 is deprotonated while Glu108 is reprotonated to regenerate the native state of the enzyme.

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Catalytic Residues Roles

Residue Roles
Glu108A proton acceptor
His39A proton donor

Chemical Components

proton transfer, inferred reaction step
Download: Image, Marvin File

Step 1. His39 deprotonates the hydroxyl group of the substrate. A hydride is transferred from the C2 of the substrate to C5 of F420. The oxidised product is formed.

Step 2. Glu108 protonates N10 of the reduced F420 cofactor.

Step 3. In an inferred step His39 is deprotonated while Glu108 is reprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, Amelia Brasnett