NAD-dependent formate dehydrogenase

 

NAD-dependent formate dehydrogenase (FDH) catalyses the NAD+-dependent oxidation of a formate anion to carbon dioxide coupled with the reduction of NAD+ to NADH. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family have two highly similar subdomains of the alpha/beta form, with NAD binding occurring in the cleft between subdomains. NAD contacts are primarily to the Rossmann-fold NAD-binding domain which is inserted within the linear sequence of the more diverse flavodoxin-like catalytic subdomain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production from C1 compounds such as methanol, and in the stress responses of plants [PMID:9178506, PMID:12144528, PMID:11921099]. NAD-dependent FDH is useful in cofactor regeneration in asymmetrical biocatalytic reduction processes, where FDH irreversibly oxidises formate to carbon dioxide, while reducing the oxidised form of the cofactor to the reduced form.

 

Reference Protein and Structure

Sequence
P33160 UniProt (1.17.1.9) IPR033689 (Sequence Homologues) (PDB Homologues)
Biological species
Pseudomonas sp. 101 (Bacteria) Uniprot
PDB
2nac - HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE (1.8 Å) PDBe PDBsum 2nac
Catalytic CATH Domains
3.40.50.720 CATHdb (see all for 2nac)
Click To Show Structure

Enzyme Reaction (EC:1.17.1.9)

formate
CHEBI:15740ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
→
carbon dioxide
CHEBI:16526ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
Alternative enzyme names: FDH I, FDH II, N-FDH, NAD(+)-dependent formate dehydrogenase, NAD(+)-formate dehydrogenase, NAD(+)-linked formate dehydrogenase, Formate benzyl-viologen oxidoreductase, Formate dehydrogenase (NAD(+)), Formate hydrogenlyase, Formate-NAD(+) oxidoreductase, Formic acid dehydrogenase, Formic hydrogen-lyase, Hydrogenlyase,

Enzyme Mechanism

Introduction

In the transition state of this reaction, a hydride ion leaves the formate and attacks the C4N of the positively charge nicotinamide moiety of NAD. The active site of the protein serves to modify the electrostatics to favour the neutral species, rather than the charged ones.

Catalytic Residues Roles

UniProt PDB* (2nac)
Asn147, Arg285 Asn146A, Arg284A Acts to stabilise the negatively charged transition states and intermediates formed during the course of the reaction. electrostatic stabiliser
Gln314 Gln313A Forms a hydrogen bond with His332, ensures that the His residue is in a neutral state. modifies pKa
His333 His332A Thought to perturb the NAD nicotinamide unit, enhancing the reactivity of the hydride transfer. enhance reactivity
*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

References

  1. Lamzin VS et al. (1994), J Mol Biol, 236, 759-785. High resolution structures of holo and apo formate dehydrogenase. DOI:10.1006/jmbi.1994.1188. PMID:8114093.
  2. Nilov DK et al. (2012), J Biomol Struct Dyn, 30, 170-179. Molecular modeling of formate dehydrogenase: the formation of the Michaelis complex. DOI:10.1080/07391102.2012.677768. PMID:22702728.
  3. Tishkov VI et al. (2004), Biochemistry (Mosc), 69, 1252-1267. Catalytic mechanism and application of formate dehydrogenase. PMID:15627379.
  4. Serov AE et al. (2002), Biochem J, 367, 841-847. Engineering of coenzyme specificity of formate dehydrogenase from Saccharomyces cerevisiae. DOI:10.1042/BJ20020379. PMID:12144528.
  5. Overkamp KM et al. (2002), Yeast, 19, 509-520. Functional analysis of structural genes for NAD(+)-dependent formate dehydrogenase in Saccharomyces cerevisiae. DOI:10.1002/yea.856. PMID:11921099.
  6. van den Berg MA et al. (1997), Yeast, 13, 551-559. Expression cassettes for formaldehyde and fluoroacetate resistance, two dominant markers in Saccharomyces cerevisiae. DOI:10.1002/(SICI)1097-0061(199705)13:6<551::AID-YEA113>3.0.CO;2-0. PMID:9178506.
  7. Tishkov VI et al. (1996), FEBS Lett, 390, 104-108. Site-directed mutagenesis of the formate dehydrogenase active centre: role of the His332-Gln313pair in enzyme catalysis. DOI:10.1016/0014-5793(96)00641-2. PMID:8706817.

Step 1.

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Catalytic Residues Roles

Residue Roles
Arg284A electrostatic stabiliser
Gln313A modifies pKa
His332A enhance reactivity
Asn146A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Craig Porter, Gemma L. Holliday