EzCatDB: D00146

DB codeD00146
RLCP classification1.15.9500.580
CATH domainDomain 12.60.40.380
Domain 23.60.21.10Catalytic domain
E.C.3.1.3.2
CSA4kbp
MACiEM0043

CATH domainRelated DB codes (homologues)
3.60.21.10D00147,D00151,S00435

Enzyme Name
Swiss-protKEGG

P80366
Protein nameFe(3+)-Zn(2+) purple acid phosphatase (PAP) (EC 3.1.3.2) (Ironacid phosphatase
acid phosphomonoesterase
phosphomonoesterase
glycerophosphatase
acid monophosphatase
acid phosphohydrolase
acid phosphomonoester hydrolase
uteroferrin
acid nucleoside diphosphate phosphatase
orthophosphoric-monoester phosphohydrolase (acid optimum)
SynonymsIII)-zinc(II) purple acid phosphatase

KEGG pathways
MAP codePathways
MAP00361gamma-Hexachlorocyclohexane degradation
MAP00740Riboflavin metabolism

Swiss-prot:Accession NumberP80366
Entry namePPAF_PHAVU
ActivityA phosphate monoester + H(2)O = an alcohol + phosphate.
SubunitHomodimer, disulfide-linked.
Subcellular locationSecreted.
CofactorBinds 1 iron ion per subunit.,Binds 1 zinc ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00023C00038C01153C00001C00069C00009
CompoundIronZincOrthophosphoric monoesterH2OAlcoholOrthophosphate
Typeheavy metalheavy metalcarbohydrate,phosphate group/phosphate ionH2Ocarbohydratephosphate group/phosphate ion
1kbpA01UnboundUnboundUnbound
UnboundUnbound
1kbpB01UnboundUnboundUnbound
UnboundUnbound
1kbpC01UnboundUnboundUnbound
UnboundUnbound
1kbpD01UnboundUnboundUnbound
UnboundUnbound
3kbpA01UnboundUnboundUnbound
UnboundUnbound
3kbpB01UnboundUnboundUnbound
UnboundUnbound
3kbpC01UnboundUnboundUnbound
UnboundUnbound
3kbpD01UnboundUnboundUnbound
UnboundUnbound
4kbpA01UnboundUnboundUnbound
UnboundUnbound
4kbpB01UnboundUnboundUnbound
UnboundUnbound
4kbpC01UnboundUnboundUnbound
UnboundUnbound
4kbpD01UnboundUnboundUnbound
UnboundUnbound
1kbpA02Bound:_FEBound:_ZNUnbound
UnboundUnbound
1kbpB02Bound:_FEBound:_ZNUnbound
UnboundUnbound
1kbpC02Bound:_FEBound:_ZNUnbound
UnboundUnbound
1kbpD02Bound:_FEBound:_ZNUnbound
UnboundUnbound
3kbpA02Bound:_FEBound:_ZNUnbound
UnboundAnalogue:WO4
3kbpB02Bound:_FEBound:_ZNUnbound
UnboundAnalogue:WO4
3kbpC02Bound:_FEBound:_ZNUnbound
UnboundAnalogue:WO4
3kbpD02Bound:_FEBound:_ZNUnbound
UnboundAnalogue:WO4
4kbpA02Bound:_FEBound:_ZNUnbound
UnboundBound:PO4
4kbpB02Bound:_FEBound:_ZNUnbound
UnboundBound:PO4
4kbpC02Bound:_FEBound:_ZNUnbound
UnboundBound:PO4
4kbpD02Bound:_FEBound:_ZNUnbound
UnboundBound:PO4

Active-site residues
resource
Swiss-prot & literature
pdbCatalytic residuesCofactor-binding residues
1kbpA01

1kbpB01

1kbpC01

1kbpD01

3kbpA01

3kbpB01

3kbpC01

3kbpD01

4kbpA01

4kbpB01

4kbpC01

4kbpD01

1kbpA02HIS 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)
1kbpB02HIS 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)
1kbpC02HIS 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)
1kbpD02HIS 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)
3kbpA02HIS 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)
3kbpB02HIS 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)
3kbpC02HIS 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)
3kbpD02HIS 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)
4kbpA02HIS 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)
4kbpB02HIS 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)
4kbpC02HIS 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)
4kbpD02HIS 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
ReferencesSectionsNo. of steps in catalysis
[5]p.1490-1491
[6]Fig.6, p.740-7443
[11]p.203-208
[13]p.9923-9924, Scheme 3
[15]Fig.8, p.143-1442
[20]p.5643

references
[1]
PubMed ID1648483
JournalEur J Biochem
Year1991
Volume199
Pages105-13
AuthorsDietrich M, Munstermann D, Suerbaum H, Witzel H
TitlePurple acid phosphatase from bovine spleen. Interactions at the active site in relation to the reaction mechanism.
[2]
PubMed ID1332769
JournalBiochemistry
Year1992
Volume31
Pages11731-9
AuthorsCrans DC, Simone CM, Holz RC, Que L Jr
TitleInteraction of porcine uterine fluid purple acid phosphatase with vanadate and vanadyl cation.
[3]
PubMed ID7821667
JournalBiochem Soc Trans
Year1994
Volume22
Pages700-4
AuthorsWilkins PC, Dalton H
TitleVariations on a theme of Fe-O-Fe proteins.
[4]
PubMed ID7771777
JournalArch Biochem Biophys
Year1995
Volume319
Pages133-41
AuthorsWynne CJ, Hamilton SE, Dionysius DA, Beck JL, de Jersey J
TitleStudies on the catalytic mechanism of pig purple acid phosphatase.
[5]
PubMed ID7770774
JournalScience
Year1995
Volume268
Pages1489-92
AuthorsStrater N, Klabunde T, Tucker P, Witzel H, Krebs B
TitleCrystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site.
[6]
CommentsX-ray crystallography
Medline ID96275658
PubMed ID8683579
JournalJ Mol Biol
Year1996
Volume259
Pages737-48
AuthorsKlabunde T, Strater N, Frohlich R, Witzel H, Krebs B
TitleMechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures.
Related PDB1kbp,3kbp,4kbp
Related Swiss-protP80366
[7]
PubMed ID9020859
JournalBiochem J
Year1997
Volume321
Pages305-11
AuthorsEk-Rylander B, Barkhem T, Ljusberg J, Ohman L, Andersson KK, Andersson G
TitleComparative studies of rat recombinant purple acid phosphatase and bone tartrate-resistant acid phosphatase.
[8]
PubMed ID9169589
JournalBiochem J
Year1997
Volume323
Pages593-6
AuthorsBattistuzzi G, Dietrich M, Locke R, Witzel H
TitleEvidence 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.
[9]
PubMed ID9698368
JournalBiochemistry
Year1998
Volume37
Pages11223-31
AuthorsMerkx M, Averill BA
TitleThe activity of oxidized bovine spleen purple acid phosphatase is due to an Fe(III)Zn(II) 'impurity'.
[10]
PubMed ID10376348
JournalJ Inorg Biochem
Year1999
Volume73
Pages245-52
AuthorsBeck JL, Durack MC, Hamilton SE, de Jersey J
TitleIrreversible inactivation of purple acid phosphatase by hydrogen peroxide and ascorbate.
[11]
CommentsX-ray crystallography (2.7 Angstroms)
PubMed ID10388567
JournalJ Mol Biol
Year1999
Volume290
Pages201-11
AuthorsUppenberg J, Lindqvist F, Svensson C, Ek-Rylander B, Andersson G
TitleCrystal structure of a mammalian purple acid phosphatase.
Related PDB1qfc
[12]
CommentsX-ray crystallography (1.55 Angstroms)
PubMed ID10425678
JournalStructure Fold Des
Year1999
Volume7
Pages757-67
AuthorsGuddat LW, McAlpine AS, Hume D, Hamilton S, de Jersey J, Martin JL
TitleCrystal structure of mammalian purple acid phosphatase.
Related PDB1ute
[13]
PubMed ID10433698
JournalBiochemistry
Year1999
Volume38
Pages9914-25
AuthorsMerkx M, Pinkse MW, Averill BA
TitleEvidence for nonbridged coordination of p-nitrophenyl phosphate to the dinuclear Fe(III)-M(II) center in bovine spleen purple acid phosphatase during enzymatic turnover.
[14]
PubMed ID10433699
JournalBiochemistry
Year1999
Volume38
Pages9926-36
AuthorsPinkse MW, Merkx M, Averill BA
TitleFluoride 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.
[15]
CommentsX-ray crystallography (2.2 Angstroms)
PubMed ID10438611
JournalJ Mol Biol
Year1999
Volume291
Pages135-47
AuthorsLindqvist Y, Johansson E, Kaija H, Vihko P, Schneider G
TitleThree-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center.
Related PDB1qhw
[16]
PubMed ID11278566
JournalJ Biol Chem
Year2001
Volume276
Pages19084-8
AuthorsSchenk G, Boutchard CL, Carrington LE, Noble CJ, Moubaraki B, Murray KS, de Jersey J, Hanson GR, Hamilton S
TitleA purple acid phosphatase from sweet potato contains an antiferromagnetically coupled binuclear Fe-Mn center.
[17]
PubMed ID11491293
JournalJ Mol Biol
Year2001
Volume309
Pages239-54
AuthorsKnofel T, Strater N
TitleMechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
[18]
PubMed ID11560512
JournalBiochemistry
Year2001
Volume40
Pages11614-22
AuthorsFunhoff EG, Ljusberg J, Wang Y, Andersson G, Averill BA
TitleMutational analysis of the interaction between active site residues and the loop region in mammalian purple acid phosphatases.
[19]
PubMed ID11828464
JournalChembiochem
Year2001
Volume2
Pages355-63
AuthorsFunhoff EG, Klaassen CH, Samyn B, Van Beeumen J, Averill BA
TitleThe highly exposed loop region in mammalian purple acid phosphatase controls the catalytic activity.
[20]
PubMed ID12401063
JournalInorg Chem
Year2002
Volume41
Pages5641-3
AuthorsLanznaster M, Neves A, Bortoluzzi AJ, Szpoganicz B, Schwingel E
TitleNew 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.
[21]
PubMed ID12440878
JournalJ Am Chem Soc
Year2002
Volume124
Pages13974-5
AuthorsDikiy A, Funhoff EG, Averill BA, Ciurli S
TitleNew insights into the mechanism of purple acid phosphatase through (1)H NMR spectroscopy of the recombinant human enzyme.
[22]
PubMed ID12484780
JournalBiochemistry
Year2002
Volume41
Pages15404-9
AuthorsReiter TA, Reiter NJ, Rusnak F
TitleMn2+ is a native metal ion activator for bacteriophage lambda protein phosphatase.
[23]
PubMed ID12693232
JournalInorg Chem
Year2003
Volume42
Pages499-507
AuthorsVerge F, Lebrun C, Fontecave M, Menage S
TitleHydrolysis of phosphodiesters by diiron complexes: design of nonequivalent iron sites in purple acid phosphatase models.

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]).

createdupdated
2002-07-092009-02-26


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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