Alcohol dehydrogenase (class III)

 

Class III alcohol dehydrogenases (ADH3) tend to show poor activity for ethanol among their various substrate alcohols. They catalyze the oxidation and reduction of a wide variety of substrates that include S-(hydroxymethyl)glutathione (HMGSH, leading to it being previously assigned to EC:1.1.1.284, HMGSH dehydrogenase), S-nitrosoglutathione, and long chain primary alcohols and aldehydes [PMID:1872853].

ADH3 oxidizes HMGSH to S-formylglutathione, which is then hydrolyzed to glutathione and formate by a hydrolase [PMID:9059641, PMID:7484406]. S-(hydroxymethyl)glutathione can form spontaneously from formaldehyde and glutathione, and constitutes a cellular strategy for sequestering and metabolizing highly toxic formaldehyde [PMID:12484756].

It has been noted that the the active site is located in the cleft between the coenzyme-binding and catalytic domains. It appears that the two domains can bind in different orientations, which can effect the catalytic residues (PMID:12196016 and PMID:12484756), although the mechanism appears to remain the same - with the different orientation of the two domains allowing the different histidines to bind to the NAD(H) ribose ring.

 

Reference Protein and Structure

Sequence
P11766 UniProt (1.1.1.-, 1.1.1.1, 1.1.1.284) IPR014183 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1teh - STRUCTURE OF HUMAN LIVER CHICHI ALCOHOL DEHYDROGENASE (A GLUTATHIONE-DEPENDENT FORMALDEHYDE DEHYDROGENASE) (2.7 Å) PDBe PDBsum 1teh
Catalytic CATH Domains
3.90.180.10 CATHdb (see all for 1teh)
Cofactors
Zinc(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.1)

NAD(+)
CHEBI:15846ChEBI
+
primary alcohol
CHEBI:15734ChEBI
→
NADH
CHEBI:16908ChEBI
+
hydron
CHEBI:15378ChEBI
+
aldehyde
CHEBI:17478ChEBI
Alternative enzyme names: ADH, NAD-dependent alcohol dehydrogenase, NAD-specific aromatic alcohol dehydrogenase, NADH-alcohol dehydrogenase, NADH-aldehyde dehydrogenase, Alcohol dehydrogenase (NAD), Aldehyde reductase, Aliphatic alcohol dehydrogenase, Ethanol dehydrogenase, Primary alcohol dehydrogenase, Yeast alcohol dehydrogenase,

Enzyme Mechanism

Introduction

This reaction proceeds via a random bi-bi mechanism, thus either the cofactor or substrate may bind first. The active site is in the cleft between the two domains and has a zinc ion that coordinates the hydroxyl and carbonyl groups of the substrates and activates them for hydride transfer.

Structural studies have shown that the active-site zinc moves back and forth between two positions during the catalytic cycle of FDH. Further, the catalytic domain conformation is about midway between the open and closed conformations seen in class I ADH and undergoes very little change upon binding of the cofactor.

Once both the cofactor and substrate are bound, bulk water initiates the proton transfer pathway via HIs47 and Thr48 to ultimately abstract a proton from the substrate alcohol and initiate the hydride transfer to the NAD cofactor.

Catalytic Residues Roles

UniProt PDB* (1teh)
Thr47, His46 Thr48(46)B, His47(45)B This forms part of the proton relay pathway that connects the active site to the solvent. Acts as a general acid/base. proton shuttle (general acid/base)
Glu68 Glu68(67)B In the apo state, this binds Arg369; once both substrate and cofactor are bound, it becomes one of the zinc 1 ligands. metal ligand
Cys103, Cys100, Cys97, Cys111 Cys103(102)B, Cys100(99)B, Cys97(96)B, Cys111(110)B Forms the zinc 2 tetrahedral binding site, which is the structural zinc ion. metal ligand
Arg115 Arg115(114)B Arg114 is critical in the binding of S-hydroxymethylglutathione as well as omega-hydroxyacids. It exhibits at least two different conformations between apo and holo enzyme states. It is important for the glutathione-dependent formaldehyde dehydrogenase activity and activation of fatty acid substrates. activator
Cys45, His67, Cys174 Cys46(44)B, His67(66)B, Cys174(173)B Forms the zinc 1 binding site. The fourth position in this tetrahedral site is taken up by a water molecule in the apo state. metal ligand
Arg369 Arg369(368)B Involved in the binding and orientation of the NAD cofactor. steric role
*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. Liao Y et al. (2013), Acta Crystallogr Sect F Struct Biol Cryst Commun, 69, 967-972. Structure of formaldehyde dehydrogenase fromPseudomonas aeruginosa: the binary complex with the cofactor NAD+. DOI:10.1107/s174430911302160x. PMID:23989142.
  2. Ivkovic M et al. (2011), Arch Biochem Biophys, 506, 157-164. N-Acylethanolamines as novel alcohol dehydrogenase 3 substrates. DOI:10.1016/j.abb.2010.12.002. PMID:21144815.
  3. Hellgren M et al. (2010), Cell Mol Life Sci, 67, 3005-3015. Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3. DOI:10.1007/s00018-010-0370-2. PMID:20405162.
  4. Sanghani PC et al. (2006), Biochemistry, 45, 4819-4830. Structure−Function Relationships in Human Glutathione-Dependent Formaldehyde Dehydrogenase. Role of Glu-67 and Arg-368 in the Catalytic Mechanism†,‡. DOI:10.1021/bi052554q. PMID:16605250.
  5. Norin A et al. (2004), FEBS Lett, 559, 27-32. Class III alcohol dehydrogenase: consistent pattern complemented with the mushroom enzyme. DOI:10.1016/s0014-5793(03)01524-2.
  6. Sanghani PC et al. (2003), Chem Biol Interact, 143-144, 195-200. Structure–function relationships in human Class III alcohol dehydrogenase (formaldehyde dehydrogenase). DOI:10.1016/s0009-2797(02)00203-x.
  7. Sanghani PC et al. (2002), Biochemistry, 41, 15189-15194. Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structural Changes Associated with Ternary Complex Formation†. DOI:10.1021/bi026705q. PMID:12484756.
  8. Sanghani PC et al. (2002), Biochemistry, 41, 10778-10786. Human Glutathione-Dependent Formaldehyde Dehydrogenase. Structures of Apo, Binary, and Inhibitory Ternary Complexes†. DOI:10.1021/bi0257639. PMID:12196016.
  9. Sanghani PC et al. (2000), Biochemistry, 39, 10720-10729. Kinetic Mechanism of Human Glutathione-Dependent Formaldehyde Dehydrogenase†. DOI:10.1021/bi9929711.
  10. Yang ZN et al. (1997), J Mol Biol, 265, 330-343. Structure of human χχ alcohol dehydrogenase: a glutathione-dependent formaldehyde dehydrogenase. DOI:10.1006/jmbi.1996.0731. PMID:9018047.
  11. Uotila L et al. (1997), Adv Exp Med Biol, 414, 365-371. Expression of formaldehyde dehydrogenase and S-formylglutathione hydrolase activities in different rat tissues. PMID:9059641.
  12. Koivusalo M et al. (1995), Adv Exp Med Biol, 372, 427-433. Purification and characterization of S-formylglutathione hydrolase from human, rat and fish tissues. PMID:7484406.
  13. Engeland K et al. (1993), Proc Natl Acad Sci U S A, 90, 2491-2494. Mutation of Arg-115 of human class III alcohol dehydrogenase: a binding site required for formaldehyde dehydrogenase activity and fatty acid activation. PMID:8460164.
  14. Holmquist B et al. (1993), Biochemistry, 32, 5139-5144. Role of arginine 115 in fatty acid activation and formaldehyde dehydrogenase activity of human class III alcohol dehydrogenase. PMID:8494891.
  15. Holmquist B et al. (1991), Biochem Biophys Res Commun, 178, 1371-1377. Human liver class III alcohol and glutathione dependent formaldehyde dehydrogenase are the same enzyme. PMID:1872853.
  16. Kaiser R et al. (1988), Biochemistry, 27, 1132-1140. Class III human liver alcohol dehydrogenase: a novel structural type equidistantly related to the class I and class II enzymes. PMID:3365377.

Step 1.

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Catalytic Residues Roles

Residue Roles
Cys46(44)B metal ligand
His67(66)B metal ligand
Cys174(173)B metal ligand
Arg115(114)B activator
Glu68(67)B metal ligand
Cys100(99)B metal ligand
Cys103(102)B metal ligand
Cys111(110)B metal ligand
Arg369(368)B steric role
His47(45)B proton shuttle (general acid/base)
Thr48(46)B proton shuttle (general acid/base)
Cys97(96)B metal ligand

Chemical Components

Step 1.

Contributors

Christian Drew, Craig Porter, Gemma L. Holliday