Histidinol dehydrogenase
L-histidinol dehydrogenase, sourced from Escherichia coli, catalyses the last two steps of histidine biosynthesis: NAD dependent oxidation of L-histidinol to L-histinaldehyde and then to L-histidine. L-histidinol dehydrogenase is a homodimeric zinc metalloenzyme with one binding site per monomer. Each monomer contains four domains- the intertwined dimer possibly results from domain swapping. Two domains display a similar incomplete Rossmann fold, suggesting an ancient event of gene duplication.
Reference Protein and Structure
- Sequence
-
P06988
(1.1.1.23)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Escherichia coli K-12 (Bacteria)
- PDB
-
1kae
- L-HISTIDINOL DEHYDROGENASE (HISD) STRUCTURE COMPLEXED WITH L-HISTIDINOL (SUBSTRATE), ZINC AND NAD (COFACTOR)
(1.7 Å)
- Catalytic CATH Domains
-
3.40.50.1980
(see all for 1kae)
- Cofactors
- Zinc(2+) (1), Nadph(4-) (1)
Enzyme Mechanism
Introduction
His 327 acts as a general base and abstracts a proton from the hydroxyl group of the substrate. NAD+ abstracts a hydride from the carbon bound to the deprotonated hydroxyl group. The carbon atom adopts an sp2 configuration, resulting in the formation of L-histinaldehyde. NADH leaves and is replaced by a second NAD+ molecule. Glu 326 acts as a general base and activates a neighbouring water molecule. The water molecule performs nucleophilic attack upon the carbonyl group of the L-histinaldehyde. Concomitantly, protonated His 327 acts as a general acid and protonates the aldehyde oxygen. The configuration of the carbon bound to the aldehyde group changes back to sp3, forming L-histidindiol. His 327 acts as a general base and deprotonates one of the hydroxyl groups. NAD+ abstracts a hydride from the carbon bound to the deprotonated hydroxyl group. This causes the formation of L-histidine with the reactive carbon adopting an sp2 configuration. Protonated His 327 acts as an acid, protonating a nearby water molecule. NADH leaves the active site and is replaced by another NAD+ molecule.
Catalytic Residues Roles
| UniProt | PDB* (1kae) | ||
| Gln259, His262, Asp360, His419 | Gln259A, His262A, Asp360A, His419B | The residues coordinate the Zn2+ ion. | metal ligand |
| Glu326 | Glu326A | Glu 326 acts as a general base and activates a neighbouring water molecule. | proton acceptor, proton donor |
| His327 | His327A | His 327 acts as a general base and abstracts a proton from the hydroxyl group of the substrate twice. It also acts as a general acid and protonates the aldehyde oxygen. | proton acceptor, proton donor |
Chemical Components
proton transfer, overall reactant used, intermediate formation, hydride transfer, aromatic bimolecular nucleophilic addition, bimolecular nucleophilic addition, overall product formed, intermediate collapse, inferred reaction step, native state of enzyme regeneratedReferences
- Barbosa JA et al. (2002), Proc Natl Acad Sci U S A, 99, 1859-1864. Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. DOI:10.1073/pnas.022476199. PMID:11842181.
Step 1. His327 deprotonates the hydroxyl group of L-histidinol. The NAD+ molecule accepts a hydride from the carbon bound to this hydroxide group in an aromatic bimolecular nucleophilic addition reaction, forming L-histindinaldehyde and NADP. The reactive carbon centre now adopts the sp2 configuration.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Gln259A | metal ligand |
| His262A | metal ligand |
| Asp360A | metal ligand |
| His419B | metal ligand |
| His327A | proton acceptor |
Chemical Components
proton transfer, overall reactant used, intermediate formation, hydride transfer, ingold: aromatic bimolecular nucleophilic addition
Step 2. Prior to this step the reduced NADH cofactor leaves and is replaced by a second NAD+ molecule. A water molecule is activated for nucleophilic attack at the L-histinaldehyde carbonyl carbon by Glu326. The aldehyde oxygen is protonated by His327 and L-histidindiol is formed. The reactive carbon centre is converted back to sp3 hybridisation.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Gln259A | metal ligand |
| His262A | metal ligand |
| Asp360A | metal ligand |
| His419B | metal ligand |
| Glu326A | proton acceptor |
| His327A | proton donor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, proton transfer, intermediate formation
Step 3. His327 abstracts a proton from one of the hydroxyl groups of L-histidiniol. The hydride attached to the reactive carbon is transferred to a second NAD+ molecule in a second aromatic bimolecular nucleophilic addition reaction, forming L-histidine and NADH. The reactive carbon now has the sp2 configuration.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Gln259A | metal ligand |
| His262A | metal ligand |
| Asp360A | metal ligand |
| His419B | metal ligand |
| His327A | proton acceptor |
Chemical Components
ingold: aromatic bimolecular nucleophilic addition, overall product formed, hydride transfer, proton transfer, intermediate collapse
Step 4. In an inferred reaction step His327 and Glu326 are deprotonated to regenerate the native state of the enzyme.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| His327A | proton donor |
| Glu326A | proton donor |
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