DB code: D00514

RLCP classification 1.15.30200.84 : Hydrolysis
CATH domain 3.40.50.1240 : Rossmann fold Catalytic domain
3.40.50.1240 : Rossmann fold
E.C. 3.1.3.2 3.1.3.26
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1240 : Rossmann fold S00365 S00363 S00366 D00460

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes RefSeq Pfam
P07102 Periplasmic AppA protein
None Phosphoanhydride phosphohydrolase
EC 3.1.3.2
pH 2.5 acid phosphatase
(AP)
4-phytase
EC 3.1.3.26
NP_415500.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489251.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00328 (His_Phos_2)
[Graphical View]

KEGG enzyme name
acid 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 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07102 PPA_ECOLI Myo-inositol hexakisphosphate + H(2)O = 1D- myo-inositol 1,2,3,5,6-pentakisphosphate + phosphate. A phosphate monoester + H(2)O = an alcohol + phosphate. Monomer. Periplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00361 gamma-Hexachlorocyclohexane degradation 3.1.3.2
MAP00562 Inositol phosphate metabolism 3.1.3.26
MAP00740 Riboflavin metabolism 3.1.3.2

Compound table
Substrates Products Intermediates
KEGG-id C01153 C01204 C00001 C00069 C04579 C00009
E.C. 3.1.3.2
3.1.3.26
3.1.3.2
3.1.3.26
3.1.3.2
3.1.3.26
3.1.3.2
3.1.3.26
Compound Orthophosphoric monoester myo-inositol hexakisphosphate H2O Alcohol 1D-myo-inositol 1,2,3,4,5-pentakisphosphate Orthophosphate
Type carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion H2O carbohydrate carbohydrate,phosphate group/phosphate ion phosphate group/phosphate ion
ChEBI 17401
15377
48405
26078
PubChem 22247451
962
1004
22486802
1dklA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dklB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dknA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:WO4
1dkpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:IHP Unbound Unbound Unbound
1dkqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:IHP Unbound Unbound Unbound
1dklA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dklB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dknA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1dkqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2],[3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dklA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers);HIS 17;ASP 304
1dklB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers);HIS 17;ASP 304
1dkmA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers);HIS 17;ASP 304
1dknA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers);HIS 17;ASP 304
1dkoA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers);HIS 17;ASP 304
1dkpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers); ;ASP 304 mutant H17A
1dkqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 16;ARG 20;ARG 92;HIS 303(Stabilizers); ;ASP 304 mutant H17A
1dklA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dklB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dkmA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dknA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dkoA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dkpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dkqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.2, Fig.3, p.141-142 3
[3]
Fig.4 2
[6]
p.111

References
[1]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8407898
Journal J Biol Chem
Year 1993
Volume 268
Pages 20744-6
Authors Lindqvist Y, Schneider G, Vihko P
Title Three-dimensional structure of rat acid phosphatase in complex with L(+)-tartrate.
Related PDB 1rpa
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8168503
Journal Eur J Biochem
Year 1994
Volume 221
Pages 139-142
Authors Lindqvist Y, Schneider G, Vihko P
Title Crystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism.
Related PDB 1rpt
Related UniProtKB
[3]
Resource
Comments active site mutation, catalysis
Medline ID
PubMed ID 8132635
Journal J Biol Chem
Year 1994
Volume 269
Pages 8971-8
Authors Ostanin K, Saeed A, Van Etten RL
Title Heterologous expression of human prostatic acid phosphatase and site-directed mutagenesis of the enzyme active site.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography (2.9 Angstroms)
Medline ID
PubMed ID 9804805
Journal J Biol Chem
Year 1998
Volume 273
Pages 30406-9
Authors LaCount MW, Handy G, Lebioda L
Title Structural origins of L(+)-tartrate inhibition of human prostatic acid phosphatase.
Related PDB 2hpa
Related UniProtKB
[5]
Resource
Comments Improvement of catalytic efficiency by site-directed mutagenesis
Medline ID
PubMed ID 11051103
Journal Arch Biochem Biophys
Year 2000
Volume 382
Pages 105-12
Authors Rodriguez E, Wood ZA, Karplus PA, Lei XG
Title Site-directed mutagenesis improves catalytic efficiency and thermostability of Escherichia coli pH 2.5 acid phosphatase/phytase expressed in Pichia pastoris.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography (2.05 Angstroms)
Medline ID 20122624
PubMed ID 10655611
Journal Nat Struct Biol
Year 2000
Volume 7
Pages 108-13
Authors Lim D, Golovan S, Forsberg CW, Jia Z
Title Crystal structures of Escherichia coli phytase and its complex with phytate.
Related PDB 1dkl 1dkm 1dkn 1dko 1dkp 1dkq
Related UniProtKB
[7]
Resource
Comments X-ray crystallography (3.1 Angstroms)
Medline ID
PubMed ID 10639192
Journal Prostate
Year 2000
Volume 42
Pages 211-8
Authors Jakob CG, Lewinski K, Kuciel R, Ostrowski W, Lebioda L
Title Crystal structure of human prostatic acid phosphatase .
Related PDB
Related UniProtKB

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.

Created Updated
2002-08-01 2009-02-26