DB code: S00231

RLCP classification 1.15.8310.1250 : Hydrolysis
CATH domain 3.20.20.140 : TIM Barrel Catalytic domain
E.C. 3.1.8.1
CSA 1ez2
M-CSA 1ez2
MACiE M0159

CATH domain Related DB codes (homologues)
3.20.20.140 : TIM Barrel S00232 M00186 D00673 D00675 D00801 D00873 M00030 M00225 M00226

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P0A433 Parathion hydrolase
EC 3.1.8.1
Phosphotriesterase
PTE
PF02126 (PTE)
[Graphical View]
P0A434 Parathion hydrolase
EC 3.1.8.1
Phosphotriesterase
PTE
PF02126 (PTE)
[Graphical View]

KEGG enzyme name
aryldialkylphosphatase
organophosphate hydrolase
paraoxonase
A-esterase
aryltriphosphatase
organophosphate esterase
esterase B1
esterase E4
paraoxon esterase
pirimiphos-methyloxon esterase
OPA anhydrase
organophosphorus hydrolase
phosphotriesterase
paraoxon hydrolase
OPH
organophosphorus acid anhydrase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A433 OPD_FLAS2 An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol. Homodimer (By similarity). Cell membrane, Peripheral membrane protein (By similarity). Binds 2 zinc ions per subunit (By similarity).
P0A434 OPD_BREDI An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol. Homodimer. Cell membrane, Peripheral membrane protein. Binds 2 zinc ions per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00361 gamma-Hexachlorocyclohexane degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C03254 C00001 C02534 C15584
E.C.
Compound Zinc Aryl dialkyl phosphate H2O Dialkyl phosphate Phenol
Type heavy metal aromatic ring (only carbon atom),phosphate group/phosphate ion H2O phosphate group/phosphate ion aromatic ring (only carbon atom)
ChEBI 29105
 29105
 		15377
 15377
 		15882
 15882
PubChem 32051
 32051
 		22247451
 962
 22247451
 962
 		20488062
 996
 20488062
 996
1dpmA Bound:2x_ZN Analogue:EBP_900 Bound:HOH_7 Unbound Unbound
1dpmB Bound:2x_ZN Analogue:EBP_902 Bound:HOH_17 Unbound Unbound
1eywA Bound:2x_ZN Analogue:TEN Bound:HOH_410 Unbound Unbound
1ez2A Bound:2x_ZN Analogue:DII Bound:HOH_1551 Unbound Unbound
1ez2B Bound:2x_ZN Analogue:DII Bound:HOH_2609 Unbound Unbound
1hzyA Bound:2x_ZN Unbound Unbound Unbound
1hzyB Bound:2x_ZN Unbound Unbound Unbound
1i03A Analogue:2x_CD Unbound Unbound Unbound
1i03B Analogue:2x_CD Unbound Unbound Unbound
1i0bA Analogue:2x_MN Unbound Unbound Unbound
1i0bB Analogue:2x_MN Unbound Unbound Unbound
1i0dA Analogue:_ZN,_CD Unbound Unbound Unbound
1i0dB Analogue:_ZN,_CD Unbound Unbound Unbound
1jgmA Analogue:2x_CD Unbound Unbound Unbound
1jgmB Analogue:2x_CD Unbound Unbound Unbound
1p6bA Bound:3x_ZN Unbound Unbound Unbound
1p6bB Bound:3x_ZN Unbound Analogue:EFS Unbound
1p6cA Bound:2x_ZN Analogue:DII Bound:HOH_205 Unbound Unbound
1p6cB Bound:2x_ZN Analogue:DII Bound:HOH_16 Unbound Unbound
1pscA Analogue:2x_CD Unbound Unbound Unbound
1pscB Analogue:2x_CD Unbound Unbound Unbound
1ptaA Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1psc, 1p6b & literature [8] & [20]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dpmA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 902(carbamylated) LYS-FMT carbamylated Lys
1dpmB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 904(carbamylated) LYS-FMT carbamylated Lys
1eywA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);KCX 169(Zinc-1 & Zinc-2) KCX 169(carbamylated) KCX carbamylated Lys
1ez2A ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);KCX 169(Zinc-1 & Zinc-2) KCX 169(carbamylated) KCX carbamylated Lys
1ez2B ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);KCX 169(Zinc-1 & Zinc-2) KCX 169(carbamylated) KCX carbamylated Lys
1hzyA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1hzyB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1i03A ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) CBX 369(carbamylated) LYS-CBX carbamylated Lys169
1i03B ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) CBX 369(carbamylated) LYS-CBX carbamylated Lys169
1i0bA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1i0bB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1i0dA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1i0dB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 369(carbamylated) LYS-FMT carbamylated Lys169
1jgmA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);KCX 169(Zinc-1 & Zinc-2) KCX 169(carbamylated) KCX carbamylated Lys
1jgmB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);KCX 169(Zinc-1 & Zinc-2) KCX 169(carbamylated) KCX carbamylated Lys
1p6bA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LCX 169(Zinc-1 & Zinc-2) LCX 169(carbamylated) LCX carbamylated Lys, mutant H254G, H257W, I303T
1p6bB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LCX 169(Zinc-1 & Zinc-2) LCX 169(carbamylated) LCX carbamylated Lys, mutant H254G, H257W, I303T
1p6cA HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LCX 169(Zinc-1 & Zinc-2) LCX 169(carbamylated) LCX carbamylated Lys, mutant H254G, H257W, I303T
1p6cB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LCX 169(Zinc-1 & Zinc-2) LCX 169(carbamylated) LCX carbamylated Lys, mutant H254G, H257W, I303T
1pscA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 901(carbamylated) LYS-FMT carbamylated Lys
1pscB ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2) FMT 902(carbamylated) LYS-FMT carbamylated Lys
1ptaA ASP 301 HIS 55;HIS 57;ASP 301(Zinc-1);HIS 201;HIS 230(Zinc-2);LYS 169(Zinc-1 & Zinc-2)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.6, p.21502
[3]
p.9154
[4]
p.15005
[8]
p.7978
[9]
Fig.3, p.10908-10911
[10]
Fig.6, p.6024-6025
[12]
p.1982
[16]
Fig.6, p.17450
[17]
Scheme 12,p.87-88
[20]
p.2722

References
[1]
Resource
Comments
Medline ID
PubMed ID 2174875
Journal J Biol Chem
Year 1990
Volume 265
Pages 21498-503
Authors Dumas DP, Raushel FM
Title Chemical and kinetic evidence for an essential histidine in the phosphotriesterase from Pseudomonas diminuta.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1320014
Journal J Biol Chem
Year 1992
Volume 267
Pages 13278-83
Authors Omburo GA, Kuo JM, Mullins LS, Raushel FM
Title Characterization of the zinc binding site of bacterial phosphotriesterase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8396425
Journal Biochemistry
Year 1993
Volume 32
Pages 9148-55
Authors Omburo GA, Mullins LS, Raushel FM
Title Structural characterization of the divalent cation sites of bacterial phosphotriesterase by 113Cd NMR spectroscopy.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 95092756
PubMed ID 7999757
Journal Biochemistry
Year 1994
Volume 33
Pages 15001-7
Authors Benning MM, Kuo JM, Raushel FM, Holden HM
Title Three-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents.
Related PDB 1pta
Related UniProtKB P16648
[5]
Resource
Comments ACTIVE SITE.
Medline ID 94206935
PubMed ID 8155644
Journal Biochemistry
Year 1994
Volume 33
Pages 4265-72
Authors Kuo JM, Raushel FM
Title Identification of the histidine ligands to the binuclear metal center of phosphotriesterase by site-directed mutagenesis.
Related PDB
Related UniProtKB P16648
[6]
Resource
Comments
Medline ID
PubMed ID 7864632
Journal Arch Biochem Biophys
Year 1995
Volume 316
Pages 765-72
Authors Chae MY, Omburo GA, Lindahl PA, Raushel FM
Title Utilization of copper as a paramagnetic probe for the binuclear metal center of phosphotriesterase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 7827033
Journal Biochemistry
Year 1995
Volume 34
Pages 750-4
Authors Banzon JA, Kuo JM, Fischer DR, Stang PJ, Raushel FM
Title Histidine-254 is essential for the inactivation of phosphotriesterase with the alkynyl phosphate esters and diethyl pyrocarbonate.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 95315185
PubMed ID 7794910
Journal Biochemistry
Year 1995
Volume 34
Pages 7973-8
Authors Benning MM, Kuo JM, Raushel FM, Holden HM
Title Three-dimensional structure of the binuclear metal center of phosphotriesterase.
Related PDB 1psc
Related UniProtKB P16648
[9]
Resource
Comments
Medline ID
PubMed ID 8718883
Journal Biochemistry
Year 1996
Volume 35
Pages 10904-12
Authors Hong SB, Raushel FM
Title Metal-substrate interactions facilitate the catalytic activity of the bacterial phosphotriesterase.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID 96214508
PubMed ID 8634243
Journal Biochemistry
Year 1996
Volume 35
Pages 6020-5
Authors Vanhooke JL, Benning MM, Raushel FM, Holden HM
Title Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate.
Related PDB 1dpm
Related UniProtKB P16648
[11]
Resource
Comments
Medline ID
PubMed ID 9220990
Journal Biochemistry
Year 1997
Volume 36
Pages 9022-8
Authors Hong SB, Mullins LS, Shim H, Raushel FM
Title Mechanism-based inhibitors for the inactivation of the bacterial phosphotriesterase.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 9047295
Journal Biochemistry
Year 1997
Volume 36
Pages 1982-8
Authors Kuo JM, Chae MY, Raushel FM
Title Perturbations to the active site of phosphotriesterase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9325279
Journal J Biol Chem
Year 1997
Volume 272
Pages 25596-601
Authors Watkins LM, Mahoney HJ, McCulloch JK, Raushel FM
Title Augmented hydrolysis of diisopropyl fluorophosphate in engineered mutants of phosphotriesterase.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9408951
Journal Proteins
Year 1997
Volume 29
Pages 553-61
Authors Watkins LM, Kuo JM, Chen-Goodspeed M, Raushel FM
Title A combinatorial library for the binuclear metal center of bacterial phosphotriesterase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9548740
Journal Biochemistry
Year 1998
Volume 37
Pages 5096-106
Authors Buchbinder JL, Stephenson RC, Dresser MJ, Pitera JW, Scanlan TS, Fletterick RJ
Title Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 9651332
Journal J Biol Chem
Year 1998
Volume 273
Pages 17445-50
Authors Shim H, Hong SB, Raushel FM
Title Hydrolysis of phosphodiesters through transformation of the bacterial phosphotriesterase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10800593
Journal Adv Enzymol Relat Areas Mol Biol
Year 2000
Volume 74
Pages 51-93
Authors Raushel FM, Holden HM
Title Phosphotriesterase: an enzyme in search of its natural substrate.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11118318
Journal Biochem Biophys Res Commun
Year 2000
Volume 279
Pages 516-9
Authors Gopal S, Rastogi V, Ashman W, Mulbry W
Title Mutagenesis of organophosphorus hydrolase to enhance hydrolysis of the nerve agent VX.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10871616
Journal J Biol Chem
Year 2000
Volume 275
Pages 30556-60
Authors Benning MM, Hong SB, Raushel FM, Holden HM
Title The binding of substrate analogs to phosphotriesterase.
Related PDB 1eyw 1ez2
Related UniProtKB
[20]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11258882
Journal Biochemistry
Year 2001
Volume 40
Pages 2712-22
Authors Benning MM, Shim H, Raushel FM, Holden HM
Title High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta.
Related PDB 1hzy 1i0b 1i0d 1i03 1jgm
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11170459
Journal Biochemistry
Year 2001
Volume 40
Pages 1325-31
Authors Chen-Goodspeed M, Sogorb MA, Wu F, Hong SB, Raushel FM
Title Structural determinants of the substrate and stereochemical specificity of phosphotriesterase.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11170460
Journal Biochemistry
Year 2001
Volume 40
Pages 1332-9
Authors Chen-Goodspeed M, Sogorb MA, Wu F, Raushel FM
Title Enhancement, relaxation, and reversal of the stereoselectivity for phosphotriesterase by rational evolution of active site residues.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11456615
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 817-26
Authors Koca J, Zhan CG, Rittenhouse RC, Ornstein RL
Title Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 11206385
Journal J Chem Inf Comput Sci
Year 2001
Volume 41
Pages 8-17
Authors Krauss M
Title Ab initio structure of the active site of phosphotriesterase.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11599021
Journal Proteins
Year 2001
Volume 45
Pages 183-9
Authors Pang YP
Title Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11929226
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 3498-9
Authors Li WS, Li Y, Hill CM, Lum KT, Raushel FM
Title Enzymatic synthesis of chiral organophosphothioates from prochiral precursors.
Related PDB
Related UniProtKB
[27]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15369336
Journal J Am Chem Soc
Year 2003
Volume 125
Pages 8990-1
Authors Hill CM, Li WS, Thoden JB, Holden HM, Raushel FM
Title Enhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site.
Related PDB 1p6b 1p6c
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12548728
Journal J Comput Chem
Year 2003
Volume 24
Pages 368-78
Authors Koca J, Zhan CG, Rittenhouse RC, Ornstein RL
Title Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 15018612
Journal Biochem J
Year 2004
Volume 380
Pages 627-33
Authors Rochu D, Viguie N, Renault F, Crouzier D, Froment MT, Masson P
Title Contribution of the active-site metal cation to the catalytic activity and to the conformational stability of phosphotriesterase: temperature- and pH-dependence.
Related PDB
Related UniProtKB

Comments
This enzyme is activated in vitro by the addition of carbon dioxide, which carbamates the sidechain of Lys169, according to the literature [12]. This modified lysine residue is essential to bridge the two metal cofactors.
Although early work (literature [1] & [4]) suggested that a general base to activate a water molecule, the water can be activated by the metal cofactor without any general base, according to the more recent literature ([8], [9], [10], [14]).
In any case, the metal cofactors play the following roles (see [9]):
(a) They can decrease pKa of th bound wate, increasing its nucleophilicity.
(b) They can polarize the P=O bond (or P=S bond), and thereby facilitate the approach of the attacking hydroxyl ion, by increasing the electrophilic character of the phosphoryl core.
(c) They can neutralize the development of the negative charge on the leaving group.
The most recent literature [20] and structural information suggested that the catalytic reaction of this enzyme proceeds via SN2-like mechanism as follows:
(1) Phosphoryl-oxygen bond is polarized by its interaction with zinc-2.
(2) A water or hydroxide ion bridging the two zinc ions is activated by the two zinc ions (particulary zinc-1) and Asp301 (as a general base).
(3) The activated water makes a nucleophilic attack on the phosphorus atom, releasing the leaving phenol group.

Created Updated
2005-03-10 2009-04-15