DB code: S00435

RLCP classification	1.15.9500.540 : Hydrolysis
CATH domain	3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2	Catalytic domain
E.C.	3.1.3.2
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2	D00146 D00147 D00151

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P29288	Tartrate-resistant acid phosphatase type 5	TR-AP EC 3.1.3.2 Tartrate-resistant acid ATPase TrATPase Acid phosphatase 5, tartrate resistant	NP_001257818.1 (Protein) NM_001270889.1 (DNA/RNA sequence) NP_062017.2 (Protein) NM_019144.2 (DNA/RNA sequence)	PF00149 (Metallophos) [Graphical View]
P09889	Tartrate-resistant acid phosphatase type 5	TR-AP EC 3.1.3.2 Tartrate-resistant acid ATPase TrATPase Acid phosphatase 5, tartrate resistant Uteroferrin UF	NP_999374.1 (Protein) NM_214209.1 (DNA/RNA sequence)	PF00149 (Metallophos) [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
P29288	PPA5_RAT	A phosphate monoester + H(2)O = an alcohol + phosphate.	Exists either as monomer or, after proteolytic processing, as a dimer of two chains linked by disulfide bond(s).	Lysosome.	Binds 2 iron ions per subunit.
P09889	PPA5_PIG	A phosphate monoester + H(2)O = an alcohol + phosphate.		Secreted.	Binds 2 iron ions per subunit.

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

Compound table
	Cofactors	Substrates		Products		Intermediates
KEGG-id	C00023	C01153	C00001	C00069	C00009
E.C.
Compound	Iron	Orthophosphoric monoester	H2O	Alcohol	Orthophosphate
Type	heavy metal	carbohydrate,phosphate group/phosphate ion	H2O	carbohydrate	phosphate group/phosphate ion
ChEBI	18248 82664 18248 82664		15377 15377		26078 26078
PubChem	23925 23925		22247451 962 22247451 962		1004 22486802 1004 22486802

1qfcA	Bound:2x_FE	Unbound		Unbound	Bound:PO4
1qhwA	Analogue:_FE,_ZN	Unbound		Unbound	Analogue:SO4
1uteA	Bound:FEO	Unbound		Bound:IPA	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

1qfcA	HIS 92;HIS 195;ASP 246	ASP 14;ASP 52;TYR 55;HIS 223(Fe3+ binding);ASP 52;ASN 91;HIS 186;HIS 221(Fe2+ binding)
1qhwA	HIS 113;HIS 216;ASP 267	ASP 35;ASP 73;TYR 76;HIS 244(Fe3+ binding);ASP 73;ASN 112;HIS 207;HIS 242(Fe2+ binding)
1uteA	HIS 92;HIS 195;ASP 246	ASP 14;ASP 52;TYR 55;HIS 223(Fe3+ binding);ASP 52;ASN 91;HIS 186;HIS 221(Fe2+ 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]).

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