EzCatDB D00151

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

Synonyms

EC 3.1.3.16
Calmodulin-dependent calcineurin A subunit alpha isoform
CAM-PRP catalytic subunit

PP-1A
EC 3.1.3.16

EC 3.1.3.16
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

RefSeq

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)

NP_001095176.1 (Protein)
NM_001101706.1 (DNA/RNA sequence)

NP_777212.1 (Protein)
NM_174787.2 (DNA/RNA sequence)

NP_000936.1 (Protein)
NM_000945.3 (DNA/RNA sequence)

Pfam

PF00149 (Metallophos)
[Graphical view]

PF13499 (EF_hand_5)
PF00036 (efhand)
[Graphical view]

UniProtKB:Accession Number

Entry name

PP2BA_HUMAN

PP1A_RABIT

PP2BA_BOVIN

CANB1_HUMAN

Activity

A phosphoprotein + H(2)O = a protein + phosphate.

Subunit

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.

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 location

Nucleus (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).

Cofactor

Binds 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.

Compound table: links to PDB-related databases & PoSSuM

Cofactors

Substrates

Products

KEGG-id

Compound

Iron

Zinc

Manganese

Calcium

Calmodulin

Phosphoprotein

H2O

Casein

Phenolic phosphate

Phosphoamide

Protein

Orthophosphate

Type

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

PubChem

271

Bound:_FE

Bound:_ZN

Unbound

Bound:(chain B)

Unbound

1fjmA

Unbound

Bound:2x_MN

Unbound

Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU

Unbound

1fjmB

Unbound

Bound:2x_MN

Unbound

Analogue:ACB-ARG-ADD-CAB-DAM-DAL-LEU

Unbound

1tcoA

Bound:_FE

Bound:_ZN

Unbound

Bound:(chain B)

Unbound

Bound:PO4

1auiB

Unbound

Bound:4x_CA

Unbound (itself)

Unbound

1tcoB

Unbound

Bound:4x_CA

Unbound (itself)

Unbound

Active-site residues

resource

literature [6], Swiss-prot

pdb

Catalytic residues

Cofactor-binding residues

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

p.643

p.749-750

p.409

p.10189-10190

Fig.12, p.1504-1510

references

[1]

Comments

X-ray crystallography (2.1 Angstroms)

Medline ID

95360994

PubMed ID

7543369

Journal

Cell

Year

1995

Volume

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

[2]

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

[3]

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

[4]

PubMed ID

8987393

Journal

Trends Biochem Sci

Year

1996

Volume

Pages

407-12

Authors

Barford D

Title

Molecular mechanisms of the protein serine/threonine phosphatases.

[5]

PubMed ID

9254616

Journal

Biochemistry

Year

1997

Volume

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+.

[6]

Comments

Review

PubMed ID

11015619

Journal

Physiol Rev

Year

2000

Volume

Pages

1483-521

Authors

Rusnak F, Mertz P

Title

Calcineurin: form and function.

[7]

PubMed ID

12218175

Journal

Proc Natl Acad Sci U S A

Year

2002

Volume

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.

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

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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )