EzCatDB: S00231

DB codeS00231
RLCP classification1.15.8310.1250
CATH domainDomain 13.20.20.140Catalytic domain
E.C.3.1.8.1
CSA1ez2
MACiEM0159

CATH domainRelated DB codes (homologues)
3.20.20.140S00232,M00186,D00673,D00675,D00801,D00873,M00030,M00225,M00226

Enzyme Name
Swiss-protKEGG

P0A433P0A434
Protein nameParathion hydrolaseParathion hydrolasearyldialkylphosphatase
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
SynonymsEC 3.1.8.1
Phosphotriesterase
PTE
EC 3.1.8.1
Phosphotriesterase
PTE

KEGG pathways
MAP codePathways
MAP00361gamma-Hexachlorocyclohexane degradation

Swiss-prot:Accession NumberP0A433P0A434
Entry nameOPD_FLAS2OPD_BREDI
ActivityAn aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol.An aryl dialkyl phosphate + H(2)O = dialkyl phosphate + an aryl alcohol.
SubunitHomodimer (By similarity).Homodimer.
Subcellular locationCell membrane, Peripheral membrane protein (By similarity).Cell membrane, Peripheral membrane protein.
CofactorBinds 2 zinc ions per subunit (By similarity).Binds 2 zinc ions per subunit.


CofactorsSubstratesProducts
KEGG-idC00038C03254C00001C02534C15584
CompoundZincAryl dialkyl phosphateH2ODialkyl phosphatePhenol
Typeheavy metalaromatic ring (only carbon atom),phosphate group/phosphate ionH2Ophosphate group/phosphate ionaromatic ring (only carbon atom)
1dpmABound:2x_ZNAnalogue:EBP 900Bound:HOH 7UnboundUnbound
1dpmBBound:2x_ZNAnalogue:EBP 902Bound:HOH 17UnboundUnbound
1eywABound:2x_ZNAnalogue:TENBound:HOH 410UnboundUnbound
1ez2ABound:2x_ZNAnalogue:DIIBound:HOH 1551UnboundUnbound
1ez2BBound:2x_ZNAnalogue:DIIBound:HOH 2609UnboundUnbound
1hzyABound:2x_ZNUnbound
UnboundUnbound
1hzyBBound:2x_ZNUnbound
UnboundUnbound
1i03AAnalogue:2x_CDUnbound
UnboundUnbound
1i03BAnalogue:2x_CDUnbound
UnboundUnbound
1i0bAAnalogue:2x_MNUnbound
UnboundUnbound
1i0bBAnalogue:2x_MNUnbound
UnboundUnbound
1i0dAAnalogue:_ZN,_CDUnbound
UnboundUnbound
1i0dBAnalogue:_ZN,_CDUnbound
UnboundUnbound
1jgmAAnalogue:2x_CDUnbound
UnboundUnbound
1jgmBAnalogue:2x_CDUnbound
UnboundUnbound
1p6bABound:3x_ZNUnbound
UnboundUnbound
1p6bBBound:3x_ZNUnbound
Analogue:EFSUnbound
1p6cABound:2x_ZNAnalogue:DIIBound:HOH 205UnboundUnbound
1p6cBBound:2x_ZNAnalogue:DIIBound:HOH 16UnboundUnbound
1pscAAnalogue:2x_CDUnbound
UnboundUnbound
1pscBAnalogue:2x_CDUnbound
UnboundUnbound
1ptaAUnboundUnbound
UnboundUnbound

Active-site residues
resource
PDB;1psc, 1p6b & literature [8] & [20]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
1dpmAASP 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
1dpmBASP 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
1eywAASP 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
1ez2AASP 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
1ez2BASP 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
1hzyAASP 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
1hzyBASP 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
1i03AASP 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
1i03BASP 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
1i0bAASP 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
1i0bBASP 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
1i0dAASP 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
1i0dBASP 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
1jgmAASP 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
1jgmBASP 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
1p6bAASP 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
1p6bBASP 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
1p6cBASP 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
1pscAASP 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
1pscBASP 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
1ptaAASP 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
ReferencesSectionsNo. 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]
PubMed ID2174875
JournalJ Biol Chem
Year1990
Volume265
Pages21498-503
AuthorsDumas DP, Raushel FM
TitleChemical and kinetic evidence for an essential histidine in the phosphotriesterase from Pseudomonas diminuta.
[2]
PubMed ID1320014
JournalJ Biol Chem
Year1992
Volume267
Pages13278-83
AuthorsOmburo GA, Kuo JM, Mullins LS, Raushel FM
TitleCharacterization of the zinc binding site of bacterial phosphotriesterase.
[3]
PubMed ID8396425
JournalBiochemistry
Year1993
Volume32
Pages9148-55
AuthorsOmburo GA, Mullins LS, Raushel FM
TitleStructural characterization of the divalent cation sites of bacterial phosphotriesterase by 113Cd NMR spectroscopy.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID95092756
PubMed ID7999757
JournalBiochemistry
Year1994
Volume33
Pages15001-7
AuthorsBenning MM, Kuo JM, Raushel FM, Holden HM
TitleThree-dimensional structure of phosphotriesterase: an enzyme capable of detoxifying organophosphate nerve agents.
Related PDB1pta
Related Swiss-protP16648
[5]
CommentsACTIVE SITE.
Medline ID94206935
PubMed ID8155644
JournalBiochemistry
Year1994
Volume33
Pages4265-72
AuthorsKuo JM, Raushel FM
TitleIdentification of the histidine ligands to the binuclear metal center of phosphotriesterase by site-directed mutagenesis.
Related Swiss-protP16648
[6]
PubMed ID7864632
JournalArch Biochem Biophys
Year1995
Volume316
Pages765-72
AuthorsChae MY, Omburo GA, Lindahl PA, Raushel FM
TitleUtilization of copper as a paramagnetic probe for the binuclear metal center of phosphotriesterase.
[7]
PubMed ID7827033
JournalBiochemistry
Year1995
Volume34
Pages750-4
AuthorsBanzon JA, Kuo JM, Fischer DR, Stang PJ, Raushel FM
TitleHistidine-254 is essential for the inactivation of phosphotriesterase with the alkynyl phosphate esters and diethyl pyrocarbonate.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID95315185
PubMed ID7794910
JournalBiochemistry
Year1995
Volume34
Pages7973-8
AuthorsBenning MM, Kuo JM, Raushel FM, Holden HM
TitleThree-dimensional structure of the binuclear metal center of phosphotriesterase.
Related PDB1psc
Related Swiss-protP16648
[9]
PubMed ID8718883
JournalBiochemistry
Year1996
Volume35
Pages10904-12
AuthorsHong SB, Raushel FM
TitleMetal-substrate interactions facilitate the catalytic activity of the bacterial phosphotriesterase.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
Medline ID96214508
PubMed ID8634243
JournalBiochemistry
Year1996
Volume35
Pages6020-5
AuthorsVanhooke JL, Benning MM, Raushel FM, Holden HM
TitleThree-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate.
Related PDB1dpm
Related Swiss-protP16648
[11]
PubMed ID9220990
JournalBiochemistry
Year1997
Volume36
Pages9022-8
AuthorsHong SB, Mullins LS, Shim H, Raushel FM
TitleMechanism-based inhibitors for the inactivation of the bacterial phosphotriesterase.
[12]
PubMed ID9047295
JournalBiochemistry
Year1997
Volume36
Pages1982-8
AuthorsKuo JM, Chae MY, Raushel FM
TitlePerturbations to the active site of phosphotriesterase.
[13]
PubMed ID9325279
JournalJ Biol Chem
Year1997
Volume272
Pages25596-601
AuthorsWatkins LM, Mahoney HJ, McCulloch JK, Raushel FM
TitleAugmented hydrolysis of diisopropyl fluorophosphate in engineered mutants of phosphotriesterase.
[14]
PubMed ID9408951
JournalProteins
Year1997
Volume29
Pages553-61
AuthorsWatkins LM, Kuo JM, Chen-Goodspeed M, Raushel FM
TitleA combinatorial library for the binuclear metal center of bacterial phosphotriesterase.
[15]
PubMed ID9548740
JournalBiochemistry
Year1998
Volume37
Pages5096-106
AuthorsBuchbinder JL, Stephenson RC, Dresser MJ, Pitera JW, Scanlan TS, Fletterick RJ
TitleBiochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family.
[16]
PubMed ID9651332
JournalJ Biol Chem
Year1998
Volume273
Pages17445-50
AuthorsShim H, Hong SB, Raushel FM
TitleHydrolysis of phosphodiesters through transformation of the bacterial phosphotriesterase.
[17]
PubMed ID10800593
JournalAdv Enzymol Relat Areas Mol Biol
Year2000
Volume74
Pages51-93
AuthorsRaushel FM, Holden HM
TitlePhosphotriesterase: an enzyme in search of its natural substrate.
[18]
PubMed ID11118318
JournalBiochem Biophys Res Commun
Year2000
Volume279
Pages516-9
AuthorsGopal S, Rastogi V, Ashman W, Mulbry W
TitleMutagenesis of organophosphorus hydrolase to enhance hydrolysis of the nerve agent VX.
[19]
CommentsX-ray crystallography
PubMed ID10871616
JournalJ Biol Chem
Year2000
Volume275
Pages30556-60
AuthorsBenning MM, Hong SB, Raushel FM, Holden HM
TitleThe binding of substrate analogs to phosphotriesterase.
Related PDB1eyw,1ez2
[20]
CommentsX-ray crystallography
PubMed ID11258882
JournalBiochemistry
Year2001
Volume40
Pages2712-22
AuthorsBenning MM, Shim H, Raushel FM, Holden HM
TitleHigh resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta.
Related PDB1hzy,1i0b,1i0d,1i03,1jgm
[21]
PubMed ID11170459
JournalBiochemistry
Year2001
Volume40
Pages1325-31
AuthorsChen-Goodspeed M, Sogorb MA, Wu F, Hong SB, Raushel FM
TitleStructural determinants of the substrate and stereochemical specificity of phosphotriesterase.
[22]
PubMed ID11170460
JournalBiochemistry
Year2001
Volume40
Pages1332-9
AuthorsChen-Goodspeed M, Sogorb MA, Wu F, Raushel FM
TitleEnhancement, relaxation, and reversal of the stereoselectivity for phosphotriesterase by rational evolution of active site residues.
[23]
PubMed ID11456615
JournalJ Am Chem Soc
Year2001
Volume123
Pages817-26
AuthorsKoca J, Zhan CG, Rittenhouse RC, Ornstein RL
TitleMobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation.
[24]
PubMed ID11206385
JournalJ Chem Inf Comput Sci
Year2001
Volume41
Pages8-17
AuthorsKrauss M
TitleAb initio structure of the active site of phosphotriesterase.
[25]
PubMed ID11599021
JournalProteins
Year2001
Volume45
Pages183-9
AuthorsPang YP
TitleSuccessful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method.
[26]
PubMed ID11929226
JournalJ Am Chem Soc
Year2002
Volume124
Pages3498-9
AuthorsLi WS, Li Y, Hill CM, Lum KT, Raushel FM
TitleEnzymatic synthesis of chiral organophosphothioates from prochiral precursors.
[27]
CommentsX-ray crystallography
PubMed ID15369336
JournalJ Am Chem Soc
Year2003
Volume125
Pages8990-1
AuthorsHill CM, Li WS, Thoden JB, Holden HM, Raushel FM
TitleEnhanced degradation of chemical warfare agents through molecular engineering of the phosphotriesterase active site.
Related PDB1p6b,1p6c
[28]
PubMed ID12548728
JournalJ Comput Chem
Year2003
Volume24
Pages368-78
AuthorsKoca J, Zhan CG, Rittenhouse RC, Ornstein RL
TitleCoordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics.
[29]
PubMed ID15018612
JournalBiochem J
Year2004
Volume380
Pages627-33
AuthorsRochu D, Viguie N, Renault F, Crouzier D, Froment MT, Masson P
TitleContribution of the active-site metal cation to the catalytic activity and to the conformational stability of phosphotriesterase: temperature- and pH-dependence.

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.

createdupdated
2005-03-102009-04-15


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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