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
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)
3.60.21.10 : Purple Acid Phosphatase; chain A, domain 2 D00146 D00147 S00435
1.10.238.10 : Recoverin; domain 1 M00183 M00198 M00118

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q08209 Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
EC 3.1.3.16
CAM-PRP catalytic subunit
Calmodulin-dependent calcineurin A subunit alpha isoform
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
CAM-PRP catalytic subunit
Calmodulin-dependent calcineurin A subunit alpha isoform
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

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
29105
18291
35154
29108
15377
37548
26078
PubChem 23925
32051
23930
271
22247451
962
12793
1004
22486802
1auiA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:(chain B) Unbound Unbound Unbound Unbound Unbound Unbound
1fjmA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU Unbound
1fjmB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:2x_MN Unbound Unbound Unbound Unbound Unbound Unbound Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU Unbound
1tcoA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_FE Bound:_ZN Unbound Unbound Bound:(chain B) Unbound Unbound Unbound Unbound Unbound Bound:PO4
1auiB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:4x_CA Unbound (itself) Unbound Unbound Unbound Unbound Unbound Unbound
1tcoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1tcoB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

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).

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