EzCatDB: D00151

DB codeD00151
RLCP classification1.15.14410.1770
CATH domainDomain domain

CATH domainRelated DB codes (homologues),M00198,M00118,D00147,S00435

Enzyme Name

Protein nameSerine/threonine-protein phosphatase 2B catalytic subunit alpha isoformSerine/threonine-protein phosphatase PP1-alpha catalytic subunitSerine/threonine-protein phosphatase 2B catalytic subunit alpha isoformCalcineurin subunit B type 1phosphoprotein 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
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
Calmodulin-dependent calcineurin A subunit alpha isoform
CAM-PRP catalytic subunit
Calmodulin-dependent calcineurin A subunit alpha isoform
CAM-PRP catalytic subunit
Protein phosphatase 2B regulatory subunit 1
Protein phosphatase 3 regulatory subunit B alpha isoform 1

Swiss-prot:Accession NumberQ08209P62139P48452P63098
ActivityA phosphoprotein + H(2)O = a protein + phosphate.A phosphoprotein + H(2)O = a protein + phosphate.A phosphoprotein + H(2)O = a protein + phosphate.
SubunitComposed 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.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).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).Composed of a catalytic subunit (A) and a regulatory subunit (B).
Subcellular locationNucleus (By similarity). Note=Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle (By similarity).Cytoplasm (By similarity).Nucleus (By similarity). Note=Colocalizes with ACTN1 and MYOZ2 at the Z line in heart and skeletal muscle (By similarity).
CofactorBinds 1 Fe(3+) ion per subunit.,Binds 1 zinc ion per subunit.Binds 1 iron ion per subunit.,Binds 1 manganese ion per subunit.Binds 1 Fe(3+) ion per subunit.,Binds 1 zinc ion per subunit.

CompoundIronZincManganeseCalciumCalmodulinPhosphoproteinH2OCaseinPhenolic phosphatePhosphoamideProteinOrthophosphate
Typeheavy metalheavy metalheavy metaldivalent metal (Ca2+, Mg2+)peptide/proteinpeptide/protein,phosphate group/phosphate ionH2Opeptide/protein,phosphate group/phosphate ionaromatic ring (only carbon atom),phosphate group/phosphate ionamine group,phosphate group/phosphate ionpeptide/proteinphosphate group/phosphate ion
1auiABound:_FEBound:_ZNUnboundUnboundBound:(chain B)Unbound
1tcoABound:_FEBound:_ZNUnboundUnboundBound:(chain B)Unbound
1auiBUnboundUnboundUnboundBound:4x_CAUnbound (itself)Unbound
1tcoBUnboundUnboundUnboundBound:4x_CAUnbound (itself)Unbound

Active-site residues
literature [6], Swiss-prot
pdbCatalytic residuesCofactor-binding residues
1auiAASP 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)
1fjmAASP  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)
1fjmBASP  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)
1tcoAASP 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)


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]Fig.12, p.1504-15103

CommentsX-ray crystallography (2.1 Angstroms)
Medline ID95360994
PubMed ID7543369
AuthorsGriffith JP, Kim JL, Kim EE, Sintchak MD, Thomson JA, Fitzgibbon MJ, Fleming MA, Caron PR, Hsiao K, Navia MA
TitleX-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex.
Related PDB1tco
CommentsX-ray crystallography (2.1 Angstroms, complex with FKBP12-FK506;3.5 Angstroms)
Medline ID96097077
PubMed ID8524402
AuthorsKissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW, et al
TitleCrystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex.
Related PDB1aui
CommentsX-ray crystallography (2.1 Angstroms)
Medline ID95379968
PubMed ID7651533
AuthorsGoldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J
TitleThree-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1.
Related PDB1fjm
PubMed ID8987393
JournalTrends Biochem Sci
AuthorsBarford D
TitleMolecular mechanisms of the protein serine/threonine phosphatases.
PubMed ID9254616
AuthorsHengge AC, Martin BL
TitleIsotope effect studies on the calcineurin phosphoryl-transfer reaction: transition state structure and effect of calmodulin and Mn2+.
PubMed ID11015619
JournalPhysiol Rev
AuthorsRusnak F, Mertz P
TitleCalcineurin: form and function.
PubMed ID12218175
JournalProc Natl Acad Sci U S A
AuthorsHuai Q, Kim HY, Liu Y, Zhao Y, Mondragon A, Liu JO, Ke H
TitleCrystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes.

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).


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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