EzCatDB: D00514

DB codeD00514
RLCP classification1.15.30200.84
CATH domainDomain 13.40.50.1240Catalytic domain
Domain 23.40.50.1240
E.C.3.1.3.2,3.1.3.26

CATH domainRelated DB codes (homologues)
3.40.50.1240S00365,S00363,S00366,D00460

Enzyme Name
Swiss-protKEGG

P07102
Protein namePeriplasmic appA proteinacid phosphatase
   (EC 3.1.3.2)
acid phosphomonoesterase
   (EC 3.1.3.2)
phosphomonoesterase
   (EC 3.1.3.2)
glycerophosphatase
   (EC 3.1.3.2)
acid monophosphatase
   (EC 3.1.3.2)
acid phosphohydrolase
   (EC 3.1.3.2)
acid phosphomonoester hydrolase
   (EC 3.1.3.2)
uteroferrin
   (EC 3.1.3.2)
acid nucleoside diphosphate phosphatase
   (EC 3.1.3.2)
orthophosphoric-monoester phosphohydrolase (acid optimum)
   (EC 3.1.3.2)
4-phytase
   (EC 3.1.3.26)
6-phytase (name based on 1L-numbering system and not 1D-numbering)
   (EC 3.1.3.26)
phytase
   (EC 3.1.3.26)
phytate 6-phosphatase
   (EC 3.1.3.26)
myo-inositol-hexakisphosphate 6-phosphohydrolase (name based on1L-numbering system and not 1D-numbering)
   (EC 3.1.3.26)
SynonymsNone
IncludesPhosphoanhydride phosphohydrolase
   EC 3.1.3.2
pH 2.5 acid phosphatase
(AP)
4-phytase
   EC 3.1.3.26

KEGG pathways
MAP codePathwaysE.C.
MAP00361gamma-Hexachlorocyclohexane degradation3.1.3.2
MAP00562Inositol phosphate metabolism3.1.3.26
MAP00740Riboflavin metabolism3.1.3.2

Swiss-prot:Accession NumberP07102
Entry namePPA_ECOLI
ActivityA phosphate monoester + H(2)O = an alcohol + phosphate.,Myo-inositol hexakisphosphate + H(2)O = 1D- myo-inositol 1,2,3,5,6-pentakisphosphate + phosphate.
SubunitMonomer.
Subcellular locationPeriplasm.
Cofactor


SubstratesProducts
KEGG-idC01153C01204C00001C00069C04579C00009
E.C.3.1.3.23.1.3.263.1.3.2,3.1.3.263.1.3.23.1.3.263.1.3.2,3.1.3.26
CompoundOrthophosphoric monoestermyo-inositol hexakisphosphateH2OAlcohol1D-myo-inositol 1,2,3,4,5-pentakisphosphateOrthophosphate
Typecarbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ionH2Ocarbohydratecarbohydrate,phosphate group/phosphate ionphosphate group/phosphate ion
1dklA1UnboundUnbound
UnboundUnboundUnbound
1dklB1UnboundUnbound
UnboundUnboundUnbound
1dkmA1UnboundUnbound
UnboundUnboundUnbound
1dknA1UnboundUnbound
UnboundUnboundUnbound
1dkoA1UnboundUnbound
UnboundUnboundAnalogue:WO4
1dkpA1UnboundBound:IHP
UnboundUnboundUnbound
1dkqA1UnboundBound:IHP
UnboundUnboundUnbound
1dklA2UnboundUnbound
UnboundUnboundUnbound
1dklB2UnboundUnbound
UnboundUnboundUnbound
1dkmA2UnboundUnbound
UnboundUnboundUnbound
1dknA2UnboundUnbound
UnboundUnboundUnbound
1dkoA2UnboundUnbound
UnboundUnboundUnbound
1dkpA2UnboundUnbound
UnboundUnboundUnbound
1dkqA2UnboundUnbound
UnboundUnboundUnbound

Active-site residues
resource
literature [2],[3]
pdbCatalytic residuescomment
1dklA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);HIS   17;ASP  304

1dklB1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);HIS   17;ASP  304

1dkmA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);HIS   17;ASP  304

1dknA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);HIS   17;ASP  304

1dkoA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);HIS   17;ASP  304

1dkpA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);        ;ASP  304
mutant H17A
1dkqA1ARG   16;ARG   20;ARG   92;HIS  303(Stabilizers);        ;ASP  304
mutant H17A
1dklA2

1dklB2

1dkmA2

1dknA2

1dkoA2

1dkpA2

1dkqA2


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.2, Fig.3, p.141-1423
[3]Fig.42
[6]p.111

references
[1]
CommentsX-ray crystallography
PubMed ID8407898
JournalJ Biol Chem
Year1993
Volume268
Pages20744-6
AuthorsLindqvist Y, Schneider G, Vihko P
TitleThree-dimensional structure of rat acid phosphatase in complex with L(+)-tartrate.
Related PDB1rpa
[2]
CommentsX-ray crystallography
PubMed ID8168503
JournalEur J Biochem
Year1994
Volume221
Pages139-142
AuthorsLindqvist Y, Schneider G, Vihko P
TitleCrystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism.
Related PDB1rpt
[3]
Commentsactive site mutation, catalysis
PubMed ID8132635
JournalJ Biol Chem
Year1994
Volume269
Pages8971-8
AuthorsOstanin K, Saeed A, Van Etten RL
TitleHeterologous expression of human prostatic acid phosphatase and site-directed mutagenesis of the enzyme active site.
[4]
CommentsX-ray crystallography (2.9 Angstroms)
PubMed ID9804805
JournalJ Biol Chem
Year1998
Volume273
Pages30406-9
AuthorsLaCount MW, Handy G, Lebioda L
TitleStructural origins of L(+)-tartrate inhibition of human prostatic acid phosphatase.
Related PDB2hpa
[5]
CommentsImprovement of catalytic efficiency by site-directed mutagenesis
PubMed ID11051103
JournalArch Biochem Biophys
Year2000
Volume382
Pages105-12
AuthorsRodriguez E, Wood ZA, Karplus PA, Lei XG
TitleSite-directed mutagenesis improves catalytic efficiency and thermostability of Escherichia coli pH 2.5 acid phosphatase/phytase expressed in Pichia pastoris.
[6]
CommentsX-ray crystallography (2.05 Angstroms)
Medline ID20122624
PubMed ID10655611
JournalNat Struct Biol
Year2000
Volume7
Pages108-13
AuthorsLim D, Golovan S, Forsberg CW, Jia Z
TitleCrystal structures of Escherichia coli phytase and its complex with phytate.
Related PDB1dkl,1dkm,1dkn,1dko,1dkp,1dkq
[7]
CommentsX-ray crystallography (3.1 Angstroms)
PubMed ID10639192
JournalProstate
Year2000
Volume42
Pages211-8
AuthorsJakob CG, Lewinski K, Kuciel R, Ostrowski W, Lebioda L
TitleCrystal structure of human prostatic acid phosphatase .

comments
According to the literature [2] and [3], His12 (of 1rpa/1rpt) acts as nucleophile, which attacks the phosphorous atom of the phosphate ester, whilst Asp258 protonates the leaving group. At the next stage, the deprotonated Asp258 abstracts proton from the water, which hydrolyzes the phosphorylated imidazole ring of His12 [2].
Moreover, the three positively charged arginine residues (Arg11, Arg15, Arg79) near His12 play an important role in the catalysis, as follows [2];
(1) The positive charged groups lower the pKa of the nucelophilic histidine (His12), so that the acidic phosphatase can function below pH 7.
(2) These groups will orient the phosphate group in a proper position so that the nucleophilic attack at the phosphorous atom can take place while the phosphorous-oxygen bond is cleaved.

createdupdated
2002-08-012009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/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 BIRD/Japan Science and Technology Corporation (JST) (September 2005-)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.