Aldehyde dehydrogenase (FAD-independent)
The sulfate-reducing bacteria Desulfovibrio gigas synthesises a xanthine oxidase-related molybdenum-iron protein aldehyde oxidoreductase (Mop) which catalyses the oxidation of aldehydes to carboxylic acids. Mop contains two separate [2Fe-2S] clusters, and an Mo ion held by a pterin derivative called molybdopterin cytosine dinucleotide (together called the molybedenum cofactor, Mo-co).
Reference Protein and Structure
- Sequence
-
Q46509
(1.2.99.7)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Desulfovibrio gigas (Bacteria)
- PDB
-
1vlb
- STRUCTURE REFINEMENT OF THE ALDEHYDE OXIDOREDUCTASE FROM DESULFOVIBRIO GIGAS AT 1.28 A
(1.28 Å)
- Catalytic CATH Domains
-
3.30.365.10
(see all for 1vlb)
- Cofactors
- Di-mu-sulfido-diiron(2+) (2), Mo(v)-molybdopterin cytosine dinucleotide (1) Metal MACiE
Enzyme Reaction (EC:1.2.99.7)
+
+
→
+
Alternative enzyme names: AORDd, Mop, Aldehyde oxidase, Aldehyde oxidoreductase,
Enzyme Mechanism
Introduction
The general reaction is attack of hydroxide on the aldehyde, while the terminal aldehyde hydride is transferred to the sulfido ligand of Mo. The mechanism proceeds as follows:
- In the resting enzyme, moldybdenum is Mo(VI) and coordinated to molybdopterin and water, with oxo and sulfido ligands.
- Glu 869 deprotonates the coordinated water as it attacks, as hydroxide, the electrophilic carbonyl. At the same time, the aldehyde delivers hydride to the sulfido ligand. This reduces the Mo=S bond to Mo-S, with Mo(IV) reduced to Mo(VI). The carboxylic acid product is bound to Mo(VI).
- Glu 869 coordinates to Mo(IV), with the carboxylic proton being transferred to a general base (another water molecule) and the carboxylic acid product being released from Mo(IV).
- An electron is transferred from Mo(IV) to one of the iron-sulphur clusters. Mo(IV) is thus oxidised to Mo(V).
- A second electron is transferred from Mo(V) to one of the iron-sulphur clusters. Mo(V) is thus oxidised to Mo(VI), with the sulfide proton being removed by a general base (a third water molecule) and the Mo=S bond regenerated.
Catalytic Residues Roles
| UniProt | PDB* (1vlb) | ||
| Glu869 | Glu869A | Glu 869 acts as a general base, deprotonating the nucleophilic water molecule. Glu 869 also displaces the product from Mo(IV) by coordinating to Mo(IV). |
covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleophile, proton acceptor, proton donor, metal ligand, nucleofuge |
*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 substitution, hydride transfer, bimolecular nucleophilic addition, overall reactant used, cofactor used, intermediate formation, overall product formed, hydrolysis, acidic bimolecular nucleophilic substitution, intermediate collapse, coordination to a metal ion, decoordination from a metal ion, electron transfer, native state of cofactor regenerated, electron relay, enzyme-substrate complex cleavage, intermediate terminated, native state of enzyme regeneratedReferences
- Huber R et al. (1996), Proc Natl Acad Sci U S A, 93, 8846-8851. A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes. DOI:10.1073/pnas.93.17.8846. PMID:8799115.
- Correia HD et al. (2015), J Biol Inorg Chem, 20, 219-229. Aromatic aldehydes at the active site of aldehyde oxidoreductase from Desulfovibrio gigas: reactivity and molecular details of the enzyme–substrate and enzyme–product interaction. DOI:10.1007/s00775-014-1196-4. PMID:25261288.
- Santos-Silva T et al. (2009), J Am Chem Soc, 131, 7990-7998. Kinetic, Structural, and EPR Studies Reveal That Aldehyde Oxidoreductase from Desulfovibrio gigas Does Not Need a Sulfido Ligand for Catalysis and Give Evidence for a Direct Mo−C Interaction in a Biological System. DOI:10.1021/ja809448r. PMID:19459677.
- Brondino CD et al. (2006), Curr Opin Chem Biol, 10, 109-114. Molybdenum and tungsten enzymes: the xanthine oxidase family. DOI:10.1016/j.cbpa.2006.01.034. PMID:16480912.
- Kisker C et al. (1997), Annu Rev Biochem, 66, 233-267. MOLYBDENUM-COFACTOR–CONTAINING ENZYMES:Structure and Mechanism. DOI:10.1146/annurev.biochem.66.1.233. PMID:9242907.
- Barata BA et al. (1993), Biochemistry, 32, 11559-11568. Aldehyde oxidoreductase activity in Desulfovibrio gigas: In vitro reconstitution of an electron-transfer chain from aldehydes to the production of molecular hydrogen. DOI:10.1021/bi00094a012. PMID:8218223.
Step 1. Glu869 deprotonates the water in the coordination sphere of Mo(VI), which initiates a nucleophilic attack on the aldehyde in a substitution reaction, which eliminates a hydride ion, which adds to the sulfur dianion which is also in the Mo(VI) coordination sphere, eventually reducing Mo(VI) to Mo(IV).
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu869A | hydrogen bond acceptor |
| Glu869A | proton acceptor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic substitution, hydride transfer, ingold: bimolecular nucleophilic addition, overall reactant used, cofactor used, intermediate formation, overall product formed, hydrolysis
Step 2. Water deprotonates Glu869, which initiates a nucleophilic attack on the Mo(IV) centre, displacing the carboxylic acid product in a substitution reaction.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu869A | hydrogen bond donor |
| Glu869A | proton donor, nucleophile |
Chemical Components
proton transfer, ingold: acidic bimolecular nucleophilic substitution, intermediate collapse, intermediate formation, overall product formed, coordination to a metal ion, decoordination from a metal ion
Step 3. A single electron is transferred from Mo(IV) to an acceptor via two iron-sulfur clusters.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu869A | metal ligand, covalently attached |
Chemical Components
electron transfer, overall reactant used, intermediate formation, cofactor used, native state of cofactor regenerated, electron relay
Step 4. Water deprotonates the thiolate group part of the Mo(V) coordination sphere, causing the elimination of Glu869 from the Mo(V) coordination sphere, and transfer of the second electron from Mo(V) to the acceptor via two iron-sulfur clusters.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu869A | nucleofuge |
Download: