Aldehyde dehydrogenase (NAD+) (class 2)

 

Aldehyde dehydrogenase (ALDH) catalyses the oxidation of toxic aldehydes to their corresponding acids, using NAD. The human mitochondrial form of ALDH is called class 2 ALDH.

 

Reference Protein and Structure

Sequence
P05091 UniProt (1.2.1.3) IPR015590 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1o04 - Cys302Ser mutant of human mitochondrial aldehyde dehydrogenase complexed with NAD+ and Mg2+ (1.42 Å) PDBe PDBsum 1o04
Catalytic CATH Domains
3.40.309.10 CATHdb 3.40.605.10 CATHdb (see all for 1o04)
Cofactors
Nadph(4-) (1)
Click To Show Structure

Enzyme Reaction (EC:1.2.1.3)

aldehyde
CHEBI:17478ChEBI
+
water
CHEBI:15377ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
→
hydron
CHEBI:15378ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
+
carboxylic acid
CHEBI:33575ChEBI
Alternative enzyme names: m-methylbenzaldehyde dehydrogenase, CoA-independent aldehyde dehydrogenase, NAD-aldehyde dehydrogenase, NAD-dependent 4-hydroxynonenal dehydrogenase, NAD-dependent aldehyde dehydrogenase, NAD-linked aldehyde dehydrogenase, Propionaldehyde dehydrogenase,

Enzyme Mechanism

Introduction

The catalysis follows a sequential mechanism in which NAD+ binds prior to aldehyde. The aldehyde then undergoes nucleophilic attack by Cys302, forming a covalent intermediate. Next, the carbonyl hydride is transferred to the A-side of the nicotinamide ring. In the rate-limiting step, Glu268 activates a water molecule for nucleophilic attack at the acyl-sulphur bond, releasing the acid product prior to NADH dissociation. Lys192 and Glu399 stabilise the transition state during the hydride transfer.

Catalytic Residues Roles

UniProt PDB* (1o04)
Glu285 Glu268A It acts as a base to deprotonate a water molecule for nucleophilic attack at the acyl-sulphur bond. proton acceptor, electrostatic stabiliser, proton donor
Cys319 Ser302A It acts as a nucleophile to attack the aldehyde to form a covalent enzyme-substrate intermediate. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor, electrostatic stabiliser
Lys209, Glu416 Lys192A, Glu399A It stabilises the transition state during hydride transfer from the enzyme-substrate intermediate to NAD+. 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, bimolecular nucleophilic addition, overall reactant used, intermediate formation, enzyme-substrate complex formation, aromatic bimolecular nucleophilic addition, hydride transfer, cofactor used, intermediate collapse, overall product formed, enzyme-substrate complex cleavage, inferred reaction step, native state of enzyme regenerated

References

  1. Sheikh S et al. (1997), J Biol Chem, 272, 18817-18822. The Potential Roles of the Conserved Amino Acids in Human Liver Mitochondrial Aldehyde Dehydrogenase. DOI:10.1074/jbc.272.30.18817. PMID:9228056.
  2. Ni L et al. (1997), J Biol Chem, 272, 18823-18826. Involvement of Glutamate 399 and Lysine 192 in the Mechanism of Human Liver Mitochondrial Aldehyde Dehydrogenase. DOI:10.1074/jbc.272.30.18823. PMID:9228057.
  3. Farrés J et al. (1995), Biochemistry, 34, 2592-2598. Investigation of the Active Site Cysteine Residue of Rat Liver Mitochondrial Aldehyde Dehydrogenase by Site-Directed Mutagenesis. DOI:10.1021/bi00008a025. PMID:7873540.
  4. Wang X et al. (1995), Biochemistry, 34, 237-243. Involvement of Glutamate 268 in the Active Site of Human Liver Mitochondrial (Class 2) Aldehyde Dehydrogenase As Probed by Site-Directed Mutagenesis. DOI:10.1021/bi00001a028. PMID:7819202.

Step 1. Glu268 acts as a base to abstract a proton from a water molecule which then activates Cys302.

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Catalytic Residues Roles

Residue Roles
Lys192A electrostatic stabiliser
Glu399A electrostatic stabiliser
Ser302A proton donor
Glu268A proton acceptor

Chemical Components

proton transfer

Step 2. There is nucleophilic attack on the electrophilic aldehyde by the thiolate group of Cys302, forming a tetrahedral intermediate.

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Catalytic Residues Roles

Residue Roles
Lys192A electrostatic stabiliser
Ser302A electrostatic stabiliser
Glu399A electrostatic stabiliser
Ser302A nucleophile

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, intermediate formation, enzyme-substrate complex formation

Step 3. The tetrahedral intermediate collapses and a hydride is transferred to NAD, forming NADH.

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Catalytic Residues Roles

Residue Roles
Ser302A covalently attached
Lys192A electrostatic stabiliser
Glu268A electrostatic stabiliser
Glu399A electrostatic stabiliser

Chemical Components

ingold: aromatic bimolecular nucleophilic addition, hydride transfer, cofactor used

Step 4. Glu268 activates a water molecule for nucleophilic attack on the aldehyde intermediate, eliminating Cys302 and forming the product.

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Catalytic Residues Roles

Residue Roles
Ser302A covalently attached
Lys192A electrostatic stabiliser
Ser302A electrostatic stabiliser
Glu399A electrostatic stabiliser
Glu268A proton acceptor
Ser302A nucleofuge

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, intermediate collapse, overall product formed, enzyme-substrate complex cleavage

Step 5. In an inferred reaction step Cys302 is reprotonated and Glu268 is protonated to regenerate the native state of the enzyme.

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Catalytic Residues Roles

Residue Roles
Glu268A proton donor
Ser302A proton acceptor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu268 acts as a base to abstract a proton from a water molecule which then activates Cys302.

Step 2. There is nucleophilic attack on the electrophilic aldehyde by the thiolate group of Cys302, forming a tetrahedral intermediate.

Step 3. The tetrahedral intermediate collapses and a hydride is transferred to NAD, forming NADH.

Step 4. Glu268 activates a water molecule for nucleophilic attack on the aldehyde intermediate, eliminating Cys302 and forming the product.

Step 5. In an inferred reaction step Cys302 is reprotonated and Glu268 is protonated to regenerate the native state of the enzyme.

Products.

Contributors

Mei Leung, Gemma L. Holliday, Amelia Brasnett