DB code: D00151

RLCP classification	1.15.14410.1770 : Hydrolysis
CATH domain	3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2	Catalytic domain
CATH domain	1.10.238.10 : Recoverin; domain 1
E.C.	3.1.3.16
CSA	1aui
M-CSA	1aui
MACiE

CATH domain	Related DB codes (homologues)
1.10.238.10 : Recoverin; domain 1	M00183 M00198 M00118
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2	D00146 D00147 S00435

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
Q08209	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform	EC 3.1.3.16 Calmodulin-dependent calcineurin A subunit alpha isoform CAM-PRP catalytic subunit	NP_000935.1 (Protein) NM_000944.4 (DNA/RNA sequence) NP_001124163.1 (Protein) NM_001130691.1 (DNA/RNA sequence) NP_001124164.1 (Protein) NM_001130692.1 (DNA/RNA sequence)	PF00149 (Metallophos) [Graphical View]
P62139	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	PP-1A EC 3.1.3.16	NP_001095176.1 (Protein) NM_001101706.1 (DNA/RNA sequence)	PF00149 (Metallophos) [Graphical View]
P48452	Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform	EC 3.1.3.16 Calmodulin-dependent calcineurin A subunit alpha isoform CAM-PRP catalytic subunit	NP_777212.1 (Protein) NM_174787.2 (DNA/RNA sequence)	PF00149 (Metallophos) [Graphical View]
P63098	Calcineurin subunit B type 1	Protein phosphatase 2B regulatory subunit 1 Protein phosphatase 3 regulatory subunit B alpha isoform 1	NP_000936.1 (Protein) NM_000945.3 (DNA/RNA sequence)	PF13499 (EF_hand_5) PF00036 (efhand) [Graphical View]

KEGG enzyme name
phosphoprotein phosphatase protein phosphatase-1 protein phosphatase-2A protein phosphatase-2B protein phosphatase-2C protein D phosphatase phosphospectrin phosphatase casein phosphatase Aspergillus awamori acid protein phosphatase calcineurin phosphatase 2A phosphatase 2B phosphatase II phosphatase IB phosphatase C-II polycation modulated (PCM-) phosphatase phosphopyruvate dehydrogenase phosphatase phosphatase SP branched-chain alpha-keto acid dehydrogenase phosphatase BCKDH phosphatase 3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase HMG-CoA reductase phosphatase phosphatase H-II phosphatase III phosphatase I protein phosphatase phosphatase IV

KEGG enzyme name

phosphoprotein phosphatase
protein phosphatase-1
protein phosphatase-2A
protein phosphatase-2B
protein phosphatase-2C
protein D phosphatase
phosphospectrin phosphatase
casein phosphatase
Aspergillus awamori acid protein phosphatase
calcineurin
phosphatase 2A
phosphatase 2B
phosphatase II
phosphatase IB
phosphatase C-II
polycation modulated (PCM-) phosphatase
phosphopyruvate dehydrogenase phosphatase
phosphatase SP
branched-chain alpha-keto acid dehydrogenase phosphatase
BCKDH phosphatase
3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase
HMG-CoA reductase phosphatase
phosphatase H-II
phosphatase III
phosphatase I
protein phosphatase
phosphatase IV

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
Q08209	PP2BA_HUMAN	A phosphoprotein + H(2)O = a protein + phosphate.	Composed of two components (A and B), the A component is the catalytic subunit and the B component confers calcium sensitivity. Interacts with TORC2/CRTC2, MYOZ1, MYOZ2 and MYOZ3.	Nucleus (By similarity). Note=Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle (By similarity).	Binds 1 Fe(3+) ion per subunit. Binds 1 zinc ion per subunit.
P62139	PP1A_RABIT	A phosphoprotein + H(2)O = a protein + phosphate.	PP1 comprises a catalytic subunit, PPP1CA, PPP1CB or PPP1CC, which is folded into its native form by inhibitor 2 and glycogen synthetase kinase 3, and then complexed to one or several targeting or regulatory subunits. PPP1R12A, PPP1R12B and PPP1R12C mediate binding to myosin. PPP1R3A, PPP1R3B, PPP1R3C and PPP1R3D mediate binding to glycogen. PPP1R15A and PPP1R15B mediate binding to EIF2S1. Part of a complex containing PPP1R15B, PP1 and NCK1/2. Interacts with PPP1R9A, PPP1R9B and PPP1R7 (By similarity).	Cytoplasm (By similarity).	Binds 1 iron ion per subunit. Binds 1 manganese ion per subunit.
P48452	PP2BA_BOVIN	A phosphoprotein + H(2)O = a protein + phosphate.	Composed of two components (A and B), the A component is the catalytic subunit and the B component confers calcium sensitivity. Interacts with TORC2/CRTC2, MYOZ1, MYOZ2 and MYOZ3 (By similarity).	Nucleus (By similarity). Note=Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle (By similarity).	Binds 1 Fe(3+) ion per subunit. Binds 1 zinc ion per subunit.
P63098	CANB1_HUMAN		Composed of a catalytic subunit (A) and a regulatory subunit (B).

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Cofactors					Substrates					Products		Intermediates
KEGG-id	C00023	C00038	C00034	C00076	C00391	C00562	C00001	L00078	C02734	C01976	C00017	C00009
E.C.
Compound	Iron	Zinc	Manganese	Calcium	Calmodulin	Phosphoprotein	H2O	Casein	Phenolic phosphate	Phosphoamide	Protein	Orthophosphate
Type	heavy metal	heavy metal	heavy metal	divalent metal (Ca2+, Mg2+)	peptide/protein	peptide/protein,phosphate group/phosphate ion	H2O	peptide/protein,phosphate group/phosphate ion	aromatic ring (only carbon atom),phosphate group/phosphate ion	amine group,phosphate group/phosphate ion	peptide/protein	phosphate group/phosphate ion
ChEBI	18248 82664 18248 82664	29105 29105	18291 35154 18291 35154	29108 29108			15377 15377		37548 37548			26078 26078
PubChem	23925 23925	32051 32051	23930 23930	271 271			22247451 962 22247451 962		12793 12793			1004 22486802 1004 22486802

1auiA	Bound:_FE	Bound:_ZN	Unbound	Unbound	Bound:(chain B)	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1fjmA	Unbound	Unbound	Bound:2x_MN	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU	Unbound
1fjmB	Unbound	Unbound	Bound:2x_MN	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU	Unbound
1tcoA	Bound:_FE	Bound:_ZN	Unbound	Unbound	Bound:(chain B)	Unbound		Unbound	Unbound	Unbound	Unbound	Bound:PO4
1auiB	Unbound	Unbound	Unbound	Bound:4x_CA	Unbound (itself)	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound
1tcoB	Unbound	Unbound	Unbound	Bound:4x_CA	Unbound (itself)	Unbound		Unbound	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [6], Swiss-prot

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1auiA	ASP 121;ARG 122;HIS 151;ARG 254	ASP 90;HIS 92;ASP 118(Fe binding);ASP 118;ASN 150;HIS 199;HIS 281(Zn binding)
1fjmA	ASP 95;ARG 96;HIS 125;ARG 221	ASP 64;HIS 66;ASP 92(Fe binding);ASP 92;ASN 124;HIS 173;HIS 248(Zn binding)
1fjmB	ASP 95;ARG 96;HIS 125;ARG 221	ASP 64;HIS 66;ASP 92(Fe binding);ASP 92;ASN 124;HIS 173;HIS 248(Zn binding)
1tcoA	ASP 121;ARG 122;HIS 151;ARG 254	ASP 90;HIS 92;ASP 118(Fe binding);ASP 118;ASN 150;HIS 199;HIS 281(Zn binding)
1auiB
1tcoB

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[2]	p.643
[3]	p.749-750
[4]	p.409
[5]	p.10189-10190
[6]	Fig.12, p.1504-1510	3

References
[1]
Resource
Comments	X-ray crystallography (2.1 Angstroms)
Medline ID	95360994
PubMed ID	7543369
Journal	Cell
Year	1995
Volume	82
Pages	507-522
Authors	Griffith JP, Kim JL, Kim EE, Sintchak MD, Thomson JA, Fitzgibbon MJ, Fleming MA, Caron PR, Hsiao K, Navia MA
Title	X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex.
Related PDB	1tco
Related UniProtKB
[2]
Resource
Comments	X-ray crystallography (2.1 Angstroms, complex with FKBP12-FK506;3.5 Angstroms)
Medline ID	96097077
PubMed ID	8524402
Journal	Nature
Year	1995
Volume	378
Pages	641-644
Authors	Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW, et al
Title	Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex.
Related PDB	1aui
Related UniProtKB
[3]
Resource
Comments	X-ray crystallography (2.1 Angstroms)
Medline ID	95379968
PubMed ID	7651533
Journal	Nature
Year	1995
Volume	376
Pages	745-753
Authors	Goldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J
Title	Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1.
Related PDB	1fjm
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	8987393
Journal	Trends Biochem Sci
Year	1996
Volume	21
Pages	407-12
Authors	Barford D
Title	Molecular mechanisms of the protein serine/threonine phosphatases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	9254616
Journal	Biochemistry
Year	1997
Volume	36
Pages	10185-91
Authors	Hengge AC, Martin BL
Title	Isotope effect studies on the calcineurin phosphoryl-transfer reaction: transition state structure and effect of calmodulin and Mn2+.
Related PDB
Related UniProtKB
[6]
Resource
Comments	Review
Medline ID
PubMed ID	11015619
Journal	Physiol Rev
Year	2000
Volume	80
Pages	1483-521
Authors	Rusnak F, Mertz P
Title	Calcineurin: form and function.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	12218175
Journal	Proc Natl Acad Sci U S A
Year	2002
Volume	99
Pages	12037-42
Authors	Huai Q, Kim HY, Liu Y, Zhao Y, Mondragon A, Liu JO, Ke H
Title	Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes.
Related PDB
Related UniProtKB

Comments
In this enzyme, the dinuclear metal center (Fe/Zn or Fe/Mn) seems to play a key role in the catalysis [6]. According to the paper [6], the metal coordination of the phosphate ester seems to be essential in the following functions: (a) lower the pKa of the metal-coordinated water molecule, in order to make the water nucleohilic. (b) neutralize the negative charge on the oxygen atoms of the phosphate ester, in order to increase the electrophilicity of the phosphorous atom, making it more susceptible to the nucelophilic attack. (c) orient the substrate for in-line attack. Moreover, the redox state of the iron is also important [6]. Fe3+ is required for the role as Lewis acid to lower the pKa of the bound water, whilst Fe2+ has a decreased Lewis acidity [6]. Furthermore, two arginine residues (Arg122/Arg254 for 1aui) seem to stabilize the transition state by neutralizing the negatively charged phosphate ester [6]. Although the paper [6] suggested many possible roles of His151/Asp121 (such as acid/base, substrate binding, general base, and orienting the nucleophilic hydroxide solvent molecule) in the catalysis, it proposed a dissociative (SN1-like) mechanism, where the histidine residue play a dual role as a general base and a general acid, as follows; (1) Substrate phosphoryl group might also coordinate to one or both metal ions. The two arginine residues, Arg122/Arg254, may neutralize charge by forming hydrogen bonds with the oxygen atoms of the phosphoryl group, which make the substrate more electrophilic and ready for attack by a nucleophile. (2) His151 acts as a general base to abstract proton from the metal-bound water molecule, or may orient the nucleophilic water for optimal nucleophilic attack of the phosphate ester. (3) A dissociative transition state is formed, where bond cleavage to the leaving group has occurred prior to bond formation to the nucleophile. (4) A metal-bound water hydroxide coordinated to Fe3+ acts as the attacking nucleophile, with the Fe3+ working as a Lewis acid to lower the pKa of the water. (5) P-O bond cleavage in the transition state results in a negative charge on the leaving group, which causes neutralization of the negative charge by protonation with a general acid (His151) or by coordination to a metal ion (Zn2+). Here, the two arginine residues are also important for the transition state stabilization. (6) The phosphate bridge the two metal ions of the dinuclear center. (7) The phosphate is exchanged by a solvent water molecule, which regenerates the enzyme for another turnover. On the other hand, the paper [4] suggested that the metal-bound water molecule acts as a nucleophile to attack the phosphorus atom of a phosphate group in an SN2 mechanism (associative mechanism).

Comments

In this enzyme, the dinuclear metal center (Fe/Zn or Fe/Mn) seems to play a key role in the catalysis [6]. According to the paper [6], the metal coordination of the phosphate ester seems to be essential in the following functions:
(a) lower the pKa of the metal-coordinated water molecule, in order to make the water nucleohilic.
(b) neutralize the negative charge on the oxygen atoms of the phosphate ester, in order to increase the electrophilicity of the phosphorous atom, making it more susceptible to the nucelophilic attack.
(c) orient the substrate for in-line attack.
Moreover, the redox state of the iron is also important [6]. Fe3+ is required for the role as Lewis acid to lower the pKa of the bound water, whilst Fe2+ has a decreased Lewis acidity [6].
Furthermore, two arginine residues (Arg122/Arg254 for 1aui) seem to stabilize the transition state by neutralizing the negatively charged phosphate ester [6].
Although the paper [6] suggested many possible roles of His151/Asp121 (such as acid/base, substrate binding, general base, and orienting the nucleophilic hydroxide solvent molecule) in the catalysis, it proposed a dissociative (SN1-like) mechanism, where the histidine residue play a dual role as a general base and a general acid, as follows;
(1) Substrate phosphoryl group might also coordinate to one or both metal ions. The two arginine residues, Arg122/Arg254, may neutralize charge by forming hydrogen bonds with the oxygen atoms of the phosphoryl group, which make the substrate more electrophilic and ready for attack by a nucleophile.
(2) His151 acts as a general base to abstract proton from the metal-bound water molecule, or may orient the nucleophilic water for optimal nucleophilic attack of the phosphate ester.
(3) A dissociative transition state is formed, where bond cleavage to the leaving group has occurred prior to bond formation to the nucleophile.
(4) A metal-bound water hydroxide coordinated to Fe3+ acts as the attacking nucleophile, with the Fe3+ working as a Lewis acid to lower the pKa of the water.
(5) P-O bond cleavage in the transition state results in a negative charge on the leaving group, which causes neutralization of the negative charge by protonation with a general acid (His151) or by coordination to a metal ion (Zn2+). Here, the two arginine residues are also important for the transition state stabilization.
(6) The phosphate bridge the two metal ions of the dinuclear center.
(7) The phosphate is exchanged by a solvent water molecule, which regenerates the enzyme for another turnover.
On the other hand, the paper [4] suggested that the metal-bound water molecule acts as a nucleophile to attack the phosphorus atom of a phosphate group in an SN2 mechanism (associative mechanism).

Created	Updated
2002-07-09	2012-06-26