Aryldialkylphosphatase
Phosphotriesterase (PTE) contains a binuclear zinc catalytic site, a structural motif characteristic of the amidohydrolase superfamily. The enzyme acts to hydrolyse phosphoesters via nucleophilic attack at the substrate PO bond from the bridging hydroxide ligand.
Reference Protein and Structure
- Sequence
-
P0A434
(3.1.8.1)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Brevundimonas diminuta (Bacteria)
- PDB
-
1hzy
- HIGH RESOLUTION STRUCTURE OF THE ZINC-CONTAINING PHOSPHOTRIESTERASE FROM PSEUDOMONAS DIMINUTA
(1.3 Å)
- Catalytic CATH Domains
-
3.20.20.140
(see all for 1hzy)
- Cofactors
- Zinc(2+) (2) Metal MACiE
Enzyme Reaction (EC:3.1.8.1)
+
→
+
Alternative enzyme names: A-esterase, OPA anhydrase, OPH, Aryltriphosphatase, Esterase B1, Esterase E4, Organophosphate esterase, Organophosphate hydrolase, Organophosphorus acid anhydrase, Organophosphorus hydrolase, Paraoxon esterase, Paraoxon hydrolase, Paraoxonase, Phosphotriesterase, Pirimiphos-methyloxon esterase,
Enzyme Mechanism
Introduction
The alpha zinc site induces ionisation at the water substrate through bond polarisation. The resulting nucleophilic hydroxide attacks in a SN2 fashion towards the PO bond of the phosphoester substrate. The beta zinc atom is also involved in forming the bridging hydroxide, but simmiltaneous polarisation of the phosphoester substrate, enhances the electrophillic character of the substrate and therefore the reaction rate. The residues Asp 301, Hist 254 and Asp 233 form a hydrogen bond network around the active site, facilitating proton transfer via acid/base interactions.
Catalytic Residues Roles
| UniProt | PDB* (1hzy) | ||
| Lys169 (ptm) | Lys169(136)A (ptm) | This residue is post-translationally modified to contain a carbamate group. It acts as a bridgind ligand between the two zinc binding sites. | metal ligand |
| His57, His55 | His57(24)A, His55(22)A | Forms part of the zinc 1 binding site. | metal ligand |
| His230, His201 | His230(197)A, His201(168)A | Forms part of the zinc 2 binding site. | metal ligand |
| Asp233 | Asp233(200)A | The residue forms a hydrogen bond network around the active site, facilitating proton transfer. | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| His254 | His254(221)A | The residue acts as a base within the proton transfer chain. | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| Asp301 | Asp301(268)A | The residue participates in the proton transfer chain, interacting with the His 254 and water substrate. Forms part of the zinc 1 binding site. | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
*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, overall reactant used, intermediate formation, overall product formed, proton relay, native state of enzyme regeneratedReferences
- Aubert SD et al. (2004), Biochemistry, 43, 5707-5715. Mechanism for the Hydrolysis of Organophosphates by the Bacterial Phosphotriesterase†. DOI:10.1021/bi0497805. PMID:15134445.
- Chagas MA et al. (2018), Inorg Chem, 57, 5888-5902. Base Mechanism to the Hydrolysis of Phosphate Triester Promoted by the Cd2+/Cd2+ Active site of Phosphotriesterase: A Computational Study. DOI:10.1021/acs.inorgchem.8b00361. PMID:29746110.
- Bigley AN et al. (2013), Biochim Biophys Acta, 1834, 443-453. Catalytic mechanisms for phosphotriesterases. DOI:10.1016/j.bbapap.2012.04.004. PMID:22561533.
- López-Canut V et al. (2012), Chemistry, 18, 9612-9621. Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms. DOI:10.1002/chem.201103615. PMID:22745111.
- Chen S et al. (2008), Theor Chem Acc, 120, 515-522. Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase. DOI:10.1007/s00214-008-0430-y.
- Benning, M. M. et al. (1995), Biochemistry, 34, 7973-7978. Three-dimensional structure of the binuclear metal center of phosphotriesterase. PMID:7794910.
Step 1. Asp301 deprotonates a zinc activated water, which attacks the phosphate of the aryl dialkyl phosphate in a nucleophilic substitution that releases the aryl alcohol product and the dialkyl phosphate coordinated to the active site zinc ions.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond acceptor |
| His254(221)A | hydrogen bond donor |
| Asp233(200)A | hydrogen bond acceptor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| Asp301(268)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| Asp301(268)A | proton acceptor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, intermediate formation, overall product formed
Step 2. Asp233 deprotonates His254 which deprotonates Asp301 and the dialkyl phosphate product dissociates from the active site.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond donor |
| His254(221)A | hydrogen bond acceptor, hydrogen bond donor, proton relay |
| Asp233(200)A | hydrogen bond acceptor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| Asp301(268)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| His254(221)A | proton donor, proton acceptor |
| Asp233(200)A | proton acceptor |
| Asp301(268)A | proton donor |
Chemical Components
proton transfer, proton relay
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond acceptor, metal ligand |
| His254(221)A | hydrogen bond donor |
| Asp233(200)A | hydrogen bond donor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| Asp233(200)A | proton donor |
Chemical Components
proton transfer, overall product formed
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond acceptor |
| His254(221)A | hydrogen bond donor |
| Asp233(200)A | hydrogen bond acceptor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| Asp301(268)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| Asp301(268)A | proton acceptor |
Chemical Components
proton transfer
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond acceptor, hydrogen bond donor |
| His254(221)A | hydrogen bond acceptor, hydrogen bond donor, proton relay |
| Asp233(200)A | hydrogen bond acceptor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| Asp301(268)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| Asp301(268)A | proton donor |
| His254(221)A | proton donor |
| Asp233(200)A | proton acceptor |
| His254(221)A | proton acceptor |
Chemical Components
proton transfer, proton relay
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp301(268)A | hydrogen bond acceptor |
| His254(221)A | hydrogen bond donor |
| Asp233(200)A | hydrogen bond donor |
| Lys169(136)A (ptm) | metal ligand |
| His55(22)A | metal ligand |
| His57(24)A | metal ligand |
| Asp301(268)A | metal ligand |
| His201(168)A | metal ligand |
| His230(197)A | metal ligand |
| Asp233(200)A | proton donor |
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