Histidine decarboxylase
Histidine decarboxylasses from Lactobacillus 30a is the best-studied of a class of enzyme which utilise the covalently bound cofactor, pyruvate. Models of the active site with and without the bound substrate analogue, histidine methyl ester (HisOMe), or the product, histamine, have been produced. Comparison of native and ligand-bound structures reveals no widespread differences in conformation but does reveal motion of a few key residues.
The native enzyme is an (alpha-beta)6 "hexamer". Two trimers bind bottom-to-bottom across a crystallographic dyad, forming a dumbell-shaped hexamer with cavities at either end.
Reference Protein and Structure
- Sequence
-
P00862
(4.1.1.22)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Lactobacillus sp. 30A (Bacteria)
- PDB
-
1pya
- REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A
(2.5 Å)
- Catalytic CATH Domains
-
3.50.20.10
4.10.510.10
(see all for 1pya)
Enzyme Reaction (EC:4.1.1.22)
Enzyme Mechanism
Introduction
The binding site contains two pockets, one for the imidazole group, and another one for the carboxyl -COOMe group.
The mechanism of histidine decarboxylation can be divided into three parts i) forming the Schiff base ii) decarboxylation/reprotonation iii) breaking the Schiff base.
The substrate first condenses with the pyruvoyl residue Prv-82 to form a Schiff base in which the substrate amine nitrogen is bonded to the alpha-carbon of Prv. As the carboxyl group of the substrate is removed, its negative charge passes to the alpha-carbon of the substrate, creating a transient carbanion. The Schiff base acts as a bridge - permitting resonance stabilisation of this alpha-carbon bond by the cofactor (acts as an electron sink). After the release of carbon dioxide, the alpha-carbon captures a proton from a suitable donor and the product is now ready to be freed by hydrolysis of the Schiff base.
Catalytic Residues Roles
| UniProt | PDB* (1pya) | ||
| Phe196 (main-N) | Phe195(114)F (main-N) | Helps stabilise the negatively charged intermediates and transition states. | hydrogen bond donor, electrostatic stabiliser |
| Asp64 | Asp63A | Binds the histidine substrate and helps hold it in place for the reaction to occur. | steric role |
| Glu198, Ser82 (C-term), Tyr63 | Glu197(116)F, Ser81E (C-term), Tyr62A | Acts as a general acid/base | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| Glu67 | Glu66A | Alters the pKa of the C-terminal Ser81 to act as a general acid/base. | activator, hydrogen bond acceptor |
| Ser83 (ptm) | Pyr1F (ptm) | This is a post-translationally modified residue. It acts as an electrophile, allowing the decarboxylation of histidine by forming a Schiff base with the substrate. | covalently attached, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, electron pair acceptor, electron pair donor, electrofuge, electrophile |
Chemical Components
bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, proton transfer, bimolecular elimination, enzyme-substrate complex cleavage, intermediate collapse, schiff base formed, unimolecular elimination by the conjugate base, decarboxylation, overall product formed, intermediate terminated, native state of enzyme regenerated, inferred reaction stepReferences
- Gallagher T et al. (1989), J Biol Chem, 264, 12737-12743. Pyruvoyl-dependent histidine decarboxylase. Active site structure and mechanistic analysis. PMID:2745463.
- Landete JM et al. (2008), Crit Rev Food Sci Nutr, 48, 697-714. Updated Molecular Knowledge about Histamine Biosynthesis by Bacteria. DOI:10.1080/10408390701639041. PMID:18756395.
- Schelp E et al. (2001), J Mol Biol, 306, 727-732. pH-induced structural changes regulate histidine decarboxylase activity in Lactobacillus 30a. DOI:10.1006/jmbi.2000.4430. PMID:11243783.
- Pishko EJ et al. (1993), Biochemistry, 32, 4943-4948. Site-directed alteration of three active-site residues of a pyruvoyl-dependent histidine decarboxylase. DOI:10.1021/bi00069a032. PMID:8490030.
- van Poelje PD et al. (1990), Annu Rev Biochem, 59, 29-59. Pyruvoyl-Dependent Enzymes. DOI:10.1146/annurev.bi.59.070190.000333. PMID:2197977.
Step 1. The C-terminal serine deprotonates the amine of the substrate, which attacked the terminal carbonyl carbon of the PTM pyruvoyl residue in the first step of a Schiff base formation. The oxyanion deprotonates Tyr62.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond donor |
| Glu66A | hydrogen bond acceptor, activator |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Glu197(116)F | hydrogen bond donor |
| Ser81E (C-term) | hydrogen bond acceptor |
| Pyr1F (ptm) | electrophile |
| Asp63A | steric role |
| Pyr1F (ptm) | proton acceptor |
| Ser81E (C-term) | proton acceptor |
| Tyr62A | proton donor |
Chemical Components
ingold: bimolecular nucleophilic addition, enzyme-substrate complex formation, intermediate formation, proton transfer
Step 2. Tyr62 deprotonates the newly formed secondary amine, which causes the elimination of water with concomitant deprotonation of the C-terminal serine residue, forming the Schiff base.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond acceptor |
| Ser81E (C-term) | hydrogen bond donor, hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond donor |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Pyr1F (ptm) | covalently attached, electron pair acceptor, proton acceptor |
| Asp63A | steric role |
| Ser81E (C-term) | proton donor |
| Tyr62A | proton acceptor |
Chemical Components
ingold: bimolecular elimination, proton transfer, enzyme-substrate complex cleavage, intermediate collapse, intermediate formation, schiff base formed
Step 3. The intermediate undergoes decarboxylation, with double bond rearrangement in which the pyruvoyl moiety acts as an electron sink.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond donor |
| Glu66A | hydrogen bond acceptor |
| Ser81E (C-term) | hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond donor |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Pyr1F (ptm) | electron pair acceptor, covalently attached, hydrogen bond acceptor |
| Asp63A | steric role |
Chemical Components
ingold: unimolecular elimination by the conjugate base, enzyme-substrate complex cleavage, decarboxylation, intermediate collapse, intermediate formation, overall product formed
Step 4. The oxyanion formed initiates double bond rearrangement that results in the deprotonation of Glu197F at the CA position of the covalently attached histamine.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond donor |
| Glu66A | hydrogen bond acceptor |
| Ser81E (C-term) | hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond donor |
| Phe195(114)F (main-N) | hydrogen bond donor, electrostatic stabiliser |
| Pyr1F (ptm) | electron pair donor, covalently attached, hydrogen bond acceptor, proton acceptor |
| Asp63A | steric role |
| Glu197(116)F | proton donor |
Chemical Components
proton transfer, intermediate formation
Step 5. The C-terminal serine residue deprotonates water, which in turn attacks the imine carbon in a nucleophilic addition, the nitrogen deprotonates Tyr62.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond donor |
| Glu66A | hydrogen bond acceptor, activator |
| Ser81E (C-term) | hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond acceptor |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Pyr1F (ptm) | electrophile, covalently attached, hydrogen bond acceptor, proton acceptor |
| Asp63A | steric role |
| Ser81E (C-term) | proton acceptor |
| Tyr62A | proton donor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, enzyme-substrate complex formation
Step 6. Tyr62 deprotonates the hydroxyl group of the pyruvoyl residue, which eliminated the histamine substrate with concomitant deprotonation of the C-terminal residue.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond acceptor |
| Ser81E (C-term) | hydrogen bond donor, hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond acceptor |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Pyr1F (ptm) | electrofuge, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| Asp63A | steric role |
| Ser81E (C-term) | proton donor |
| Tyr62A | proton acceptor |
| Pyr1F (ptm) | proton relay |
Chemical Components
ingold: bimolecular elimination, proton transfer, intermediate collapse, intermediate terminated, enzyme-substrate complex cleavage, overall product formed
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Tyr62A | hydrogen bond donor |
| Glu66A | hydrogen bond acceptor |
| Ser81E (C-term) | hydrogen bond acceptor |
| Glu197(116)F | hydrogen bond acceptor |
| Phe195(114)F (main-N) | hydrogen bond donor |
| Pyr1F (ptm) | hydrogen bond acceptor |
| Glu197(116)F | proton acceptor |
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