DB code: D00146

RLCP classification 1.15.9500.580 : Hydrolysis
CATH domain 2.60.40.380 : Immunoglobulin-like
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2 Catalytic domain
E.C. 3.1.3.2
CSA 4kbp
M-CSA 4kbp
MACiE M0043

CATH domain Related DB codes (homologues)
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2 D00147 D00151 S00435

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P80366 Fe(3+)-Zn(2+) purple acid phosphatase (PAP) (EC 3.1.3.2) (Iron
III)-zinc(II) purple acid phosphatase
PF00149 (Metallophos)
PF14008 (Metallophos_C)
[Graphical View]

KEGG enzyme name
acid phosphatase
acid phosphomonoesterase
phosphomonoesterase
glycerophosphatase
acid monophosphatase
acid phosphohydrolase
acid phosphomonoester hydrolase
uteroferrin
acid nucleoside diphosphate phosphatase
orthophosphoric-monoester phosphohydrolase (acid optimum)

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P80366 PPAF_PHAVU A phosphate monoester + H(2)O = an alcohol + phosphate. Homodimer, disulfide-linked. Secreted. Binds 1 iron ion per subunit. Binds 1 zinc ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00740 Riboflavin metabolism
MAP00361 gamma-Hexachlorocyclohexane degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 C00038 C01153 C00001 C00069 C00009
E.C.
Compound Iron Zinc Orthophosphoric monoester H2O Alcohol Orthophosphate
Type heavy metal heavy metal carbohydrate,phosphate group/phosphate ion H2O carbohydrate phosphate group/phosphate ion
ChEBI 18248
82664
29105
15377
26078
PubChem 23925
32051
22247451
962
1004
22486802
1kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
3kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
4kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
4kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
4kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
4kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Unbound
1kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Unbound
1kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Unbound
1kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Unbound
3kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Analogue:WO4
3kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Analogue:WO4
3kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Analogue:WO4
3kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Analogue:WO4
4kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:PO4
4kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:PO4
4kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:PO4
4kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:PO4

Reference for Active-site residues
resource references E.C.
Swiss-prot & literature

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4kbpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4kbpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4kbpC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
4kbpD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
1kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
1kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
1kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
3kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
3kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
3kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
3kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
4kbpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
4kbpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
4kbpC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)
4kbpD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 202;HIS 295;HIS 296 ASP 135;ASP 164;TYR 167;HIS 325(Fe3+ binding);ASP 164;ASN 201;HIS 286;HIS 323(Zinc binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.1490-1491
[6]
Fig.6, p.740-744 3
[11]
p.203-208
[13]
p.9923-9924, Scheme 3
[15]
Fig.8, p.143-144 2
[20]
p.5643

References
[1]
Resource
Comments
Medline ID
PubMed ID 1648483
Journal Eur J Biochem
Year 1991
Volume 199
Pages 105-13
Authors Dietrich M, Munstermann D, Suerbaum H, Witzel H
Title Purple acid phosphatase from bovine spleen. Interactions at the active site in relation to the reaction mechanism.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1332769
Journal Biochemistry
Year 1992
Volume 31
Pages 11731-9
Authors Crans DC, Simone CM, Holz RC, Que L Jr
Title Interaction of porcine uterine fluid purple acid phosphatase with vanadate and vanadyl cation.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7821667
Journal Biochem Soc Trans
Year 1994
Volume 22
Pages 700-4
Authors Wilkins PC, Dalton H
Title Variations on a theme of Fe-O-Fe proteins.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7771777
Journal Arch Biochem Biophys
Year 1995
Volume 319
Pages 133-41
Authors Wynne CJ, Hamilton SE, Dionysius DA, Beck JL, de Jersey J
Title Studies on the catalytic mechanism of pig purple acid phosphatase.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7770774
Journal Science
Year 1995
Volume 268
Pages 1489-92
Authors Strater N, Klabunde T, Tucker P, Witzel H, Krebs B
Title Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography
Medline ID 96275658
PubMed ID 8683579
Journal J Mol Biol
Year 1996
Volume 259
Pages 737-48
Authors Klabunde T, Strater N, Frohlich R, Witzel H, Krebs B
Title Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures.
Related PDB 1kbp 3kbp 4kbp
Related UniProtKB P80366
[7]
Resource
Comments
Medline ID
PubMed ID 9020859
Journal Biochem J
Year 1997
Volume 321
Pages 305-11
Authors Ek-Rylander B, Barkhem T, Ljusberg J, Ohman L, Andersson KK, Andersson G
Title Comparative studies of rat recombinant purple acid phosphatase and bone tartrate-resistant acid phosphatase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9169589
Journal Biochem J
Year 1997
Volume 323
Pages 593-6
Authors Battistuzzi G, Dietrich M, Locke R, Witzel H
Title Evidence for a conserved binding motif of the dinuclear metal site in mammalian and plant purple acid phosphatases: 1H NMR studies of the di-iron derivative of the Fe(III)Zn(II) enzyme from kidney bean.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9698368
Journal Biochemistry
Year 1998
Volume 37
Pages 11223-31
Authors Merkx M, Averill BA
Title The activity of oxidized bovine spleen purple acid phosphatase is due to an Fe(III)Zn(II) 'impurity'.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10376348
Journal J Inorg Biochem
Year 1999
Volume 73
Pages 245-52
Authors Beck JL, Durack MC, Hamilton SE, de Jersey J
Title Irreversible inactivation of purple acid phosphatase by hydrogen peroxide and ascorbate.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-ray crystallography (2.7 Angstroms)
Medline ID
PubMed ID 10388567
Journal J Mol Biol
Year 1999
Volume 290
Pages 201-11
Authors Uppenberg J, Lindqvist F, Svensson C, Ek-Rylander B, Andersson G
Title Crystal structure of a mammalian purple acid phosphatase.
Related PDB 1qfc
Related UniProtKB
[12]
Resource
Comments X-ray crystallography (1.55 Angstroms)
Medline ID
PubMed ID 10425678
Journal Structure Fold Des
Year 1999
Volume 7
Pages 757-67
Authors Guddat LW, McAlpine AS, Hume D, Hamilton S, de Jersey J, Martin JL
Title Crystal structure of mammalian purple acid phosphatase.
Related PDB 1ute
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10433698
Journal Biochemistry
Year 1999
Volume 38
Pages 9914-25
Authors Merkx M, Pinkse MW, Averill BA
Title Evidence for nonbridged coordination of p-nitrophenyl phosphate to the dinuclear Fe(III)-M(II) center in bovine spleen purple acid phosphatase during enzymatic turnover.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10433699
Journal Biochemistry
Year 1999
Volume 38
Pages 9926-36
Authors Pinkse MW, Merkx M, Averill BA
Title Fluoride inhibition of bovine spleen purple acid phosphatase: characterization of a ternary enzyme-phosphate-fluoride complex as a model for the active enzyme-substrate-hydroxide complex.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-ray crystallography (2.2 Angstroms)
Medline ID
PubMed ID 10438611
Journal J Mol Biol
Year 1999
Volume 291
Pages 135-47
Authors Lindqvist Y, Johansson E, Kaija H, Vihko P, Schneider G
Title Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center.
Related PDB 1qhw
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11278566
Journal J Biol Chem
Year 2001
Volume 276
Pages 19084-8
Authors Schenk G, Boutchard CL, Carrington LE, Noble CJ, Moubaraki B, Murray KS, de Jersey J, Hanson GR, Hamilton S
Title A purple acid phosphatase from sweet potato contains an antiferromagnetically coupled binuclear Fe-Mn center.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11491293
Journal J Mol Biol
Year 2001
Volume 309
Pages 239-54
Authors Knofel T, Strater N
Title Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11560512
Journal Biochemistry
Year 2001
Volume 40
Pages 11614-22
Authors Funhoff EG, Ljusberg J, Wang Y, Andersson G, Averill BA
Title Mutational analysis of the interaction between active site residues and the loop region in mammalian purple acid phosphatases.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11828464
Journal Chembiochem
Year 2001
Volume 2
Pages 355-63
Authors Funhoff EG, Klaassen CH, Samyn B, Van Beeumen J, Averill BA
Title The highly exposed loop region in mammalian purple acid phosphatase controls the catalytic activity.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12401063
Journal Inorg Chem
Year 2002
Volume 41
Pages 5641-3
Authors Lanznaster M, Neves A, Bortoluzzi AJ, Szpoganicz B, Schwingel E
Title New Fe(III)Zn(II) complex containing a single terminal Fe-O(phenolate) bond as a structural and functional model for the active site of red kidney bean purple acid phosphatase.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12440878
Journal J Am Chem Soc
Year 2002
Volume 124
Pages 13974-5
Authors Dikiy A, Funhoff EG, Averill BA, Ciurli S
Title New insights into the mechanism of purple acid phosphatase through (1)H NMR spectroscopy of the recombinant human enzyme.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12484780
Journal Biochemistry
Year 2002
Volume 41
Pages 15404-9
Authors Reiter TA, Reiter NJ, Rusnak F
Title Mn2+ is a native metal ion activator for bacteriophage lambda protein phosphatase.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12693232
Journal Inorg Chem
Year 2003
Volume 42
Pages 499-507
Authors Verge F, Lebrun C, Fontecave M, Menage S
Title Hydrolysis of phosphodiesters by diiron complexes: design of nonequivalent iron sites in purple acid phosphatase models.
Related PDB
Related UniProtKB

Comments
Although the purple acid phosphatases from plant (D00146) and from mammal (S00435) are homologous to each other, they adopt slightly different catalytic mechanisms. The plant enzyme uses Fe(III) and zinc ions as cofactors, whilst the mammalian enzyme uses Fe(III) and Fe(II).
According to the literature [5], [6] & [15], the catalysis proceeds through SN2-like reaction, resulting in the inversion of configuration at the phosphorous atom. This is against the covalent phosphorylated intermediate formation.
In the initial stage, the phoshate group of the substrate will bind to the divalent metal (M(II)), whilst the nucleophilic hydroxyl ion is bound to the ferric ion (Fe(III)) (see [6] & [15]). This hydroxide is in a position suitable for in-line attack on the phosphorous atom. In the first step, the hydroxyl group makes a nucleophilic attack on the phosphorous atom, forming a pentacovalent transition state, which is stablized by histidine residues, His202, His295 and His296 (plant purple acid phosphatase;PDB 1kbp), His113 and His216 (mammalian purple acid phosphatase;PDB 1qhw).
In the next step, a catalytic acid will protonate to the leaving group of the product. His296 acts as the catalytic acid in the plant enzyme (PDB 1kbp), whilst Asp267 plays the catalytic role in the mammalian enzyme (PDB 1qhw).
In the final step, the phosphate group, bound in a bidentate binding mode to the two metal ions, will be displaced from the Fe(III) ion by a coming water molecule (see [6] & [15]).

Created Updated
2002-07-09 2009-02-26