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Complex (hydrolase/isomerase) PDB id
1tco
Jmol
Contents
Protein chains
352 a.a. *
169 a.a. *
107 a.a. *
Ligands
PO4
MYR
FK5
Metals
_ZN
_FE
_CA ×4
Waters ×710
* Residue conservation analysis
PDB id:
1tco
Name: Complex (hydrolase/isomerase)
Title: Ternary complex of a calcineurin a fragment, calcineurin b, fkbp12 and the immunosuppressant drug fk506 (tacrolimus)
Structure: Serine/threonine phosphatase b2. Chain: a. Fragment: chain a is the catalytic subunit, residues 18 - 392. Chain b is the regulatory subunit, residues 1 - 169. Synonym: calcineurin a, cam-prp catalytic subunit, calcineurin b, cam-prp regulatory subunit. Engineered: yes. Serine/threonine phosphatase b2. Chain: b.
Source: Bos taurus. Cattle. Organism_taxid: 9913. Tissue: calf brain. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.195     R-free:   0.282
Authors: J.P.Griffith,J.L.Kim,E.E.Kim,M.D.Sintchak,J.A.Thomson, M.J.Fitzgibbon,M.A.Fleming,P.R.Caron,K.Hsiao,M.A.Navia
Key ref: J.P.Griffith et al. (1995). X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Cell, 82, 507-522. PubMed id: 7543369 DOI: 10.1016/0092-8674(95)90439-5
Date:
21-Aug-96     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P48452  (PP2BA_BOVIN) -  Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
Seq:
Struc: 		 
Seq:
Struc: 		521 a.a.
352 a.a.
Protein chain
Pfam   ArchSchema ?
P63099  (CANB1_BOVIN) -  Calcineurin subunit B type 1
Seq:
Struc: 		170 a.a.
169 a.a.
Protein chain
Pfam   ArchSchema ?
P18203  (FKB1A_BOVIN) -  Peptidyl-prolyl cis-trans isomerase FKBP1A
Seq:
Struc: 		108 a.a.
107 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.3.1.3.16  - Phosphoprotein phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphoprotein + H2O = a protein + phosphate
phosphoprotein
 + H(2)O
 = protein
 +
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
   Enzyme class 3: Chain C: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
 = peptidylproline (omega=0)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     muscle contraction   23 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0092-8674(95)90439-5 Cell 82:507-522 (1995)
PubMed id: 7543369  
 
 
X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex.
J.P.Griffith, J.L.Kim, E.E.Kim, M.D.Sintchak, J.A.Thomson, M.J.Fitzgibbon, M.A.Fleming, P.R.Caron, K.Hsiao, M.A.Navia.
 
  ABSTRACT  
 
The X-ray structure of the ternary complex of a calcineurin A fragment, calcineurin B, FKBP12, and the immunosuppressant drug FK506 (also known as tacrolimus) has been determined at 2.5 A resolution, providing a description of how FK506 functions at the atomic level. In the structure, the FKBP12-FK506 binary complex does not contact the phosphatase active site on calcineurin A that is more than 10 A removed. Instead, FKBP12-FK506 is so positioned that it can inhibit the dephosphorylation of its macromolecular substrates by physically hindering their approach to the active site. The ternary complex described here represents the three-dimensional structure of a Ser/Thr protein phosphatase and provides a structural basis for understanding calcineurin inhibition by FKBP12-FK506.
 

Literature references that cite this PDB file's key reference

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FK506-binding protein (FKBP) partitions a modified HIV protease inhibitor into blood cells and prolongs its lifetime in vivo.
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18688419 J.He, P.Hu, Y.J.Wang, M.L.Tong, H.Sun, Z.W.Mao, and L.N.Ji (2008).
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PDB codes: 3bof 3bol 3bq5 3bq6
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PDB code: 2r28
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PDB code: 2jog
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Structure of Streptococcus agalactiae serine/threonine phosphatase. The subdomain conformation is coupled to the binding of a third metal ion.
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PDB code: 2pk0
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Solution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1.
  J Biol Chem, 282, 2741-2751.
PDB code: 2e30
17324936 M.Saeki, Y.Irie, L.Ni, Y.Itsuki, Y.Terao, S.Kawabata, and Y.Kamisaki (2007).
Calcineurin potentiates the activation of procaspase-3 by accelerating its proteolytic maturation.
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17694572 M.Sieber, M.Karanik, C.Brandt, C.Blex, M.Podtschaske, F.Erdmann, R.Rost, E.Serfling, J.Liebscher, M.Pätzel, A.Radbruch, G.Fischer, and R.Baumgrass (2007).
Inhibition of calcineurin-NFAT signaling by the pyrazolopyrimidine compound NCI3.
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Strategies to search and design stabilizers of protein-protein interactions: a feasibility study.
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Cardiac hypertrophy: mechanisms and therapeutic opportunities.
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Structural basis for regulation of protein phosphatase 1 by inhibitor-2.
  J Biol Chem, 282, 28874-28883.
PDB codes: 2o8a 2o8g
17720810 T.Strahl, I.G.Huttner, J.D.Lusin, M.Osawa, D.King, J.Thorner, and J.B.Ames (2007).
Structural insights into activation of phosphatidylinositol 4-kinase (Pik1) by yeast frequenin (Frq1).
  J Biol Chem, 282, 30949-30959.
PDB code: 2ju0
17086192 U.S.Cho, and W.Xu (2007).
Crystal structure of a protein phosphatase 2A heterotrimeric holoenzyme.
  Nature, 445, 53-57.
PDB code: 2iae
17505522 W.J.Steinbach, J.L.Reedy, R.A.Cramer, J.R.Perfect, and J.Heitman (2007).
Harnessing calcineurin as a novel anti-infective agent against invasive fungal infections.
  Nat Rev Microbiol, 5, 418-430.  
16639748 A.M.Tokheim, and B.L.Martin (2006).
Association of calcineurin with mitochondrial proteins.
  Proteins, 64, 28-33.  
16505102 C.Marchand, S.Antony, K.W.Kohn, M.Cushman, A.Ioanoviciu, B.L.Staker, A.B.Burgin, L.Stewart, and Y.Pommier (2006).
A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex.
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16723353 C.White, J.Yang, M.J.Monteiro, and J.K.Foskett (2006).
CIB1, a ubiquitously expressed Ca2+-binding protein ligand of the InsP3 receptor Ca2+ release channel.
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Electrostatic contribution to the binding stability of protein-protein complexes.
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16547004 F.Edlich, M.Weiwad, D.Wildemann, F.Jarczowski, S.Kilka, M.C.Moutty, G.Jahreis, C.Lücke, W.Schmidt, F.Striggow, and G.Fischer (2006).
The specific FKBP38 inhibitor N-(N',N'-dimethylcarboxamidomethyl)cycloheximide has potent neuroprotective and neurotrophic properties in brain ischemia.
  J Biol Chem, 281, 14961-14970.  
17020884 J.B.Ames, K.Levay, J.N.Wingard, J.D.Lusin, and V.Z.Slepak (2006).
Structural basis for calcium-induced inhibition of rhodopsin kinase by recoverin.
  J Biol Chem, 281, 37237-37245.
PDB code: 2i94
16705489 J.D.Hoekman, A.M.Tokheim, D.J.Spannaus-Martin, and B.L.Martin (2006).
Molecular modeling of the calmodulin binding region of calcineurin.
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16844742 J.Wang, Y.Deng, and B.Roux (2006).
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.
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Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality.
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Ecto-5'-nucleotidase: Structure function relationships.
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16601955 T.Takahashi, T.Shiyama, T.Mori, K.Hosoya, and A.Tanaka (2006).
Isolating the whole complex of target proteins of FK506 using affinity resins from novel solid phases.
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17081120 X.J.Xie, C.Z.Xue, W.Huang, D.Y.Yu, and Q.Wei (2006).
The beta12-beta13 loop is a key regulatory element for the activity and properties of the catalytic domain of protein phosphatase 1 and 2B.
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15671033 A.Rodríguez, S.Martínez-Martínez, M.D.López-Maderuelo, I.Ortega-Pérez, and J.M.Redondo (2005).
The linker region joining the catalytic and the regulatory domains of CnA is essential for binding to NFAT.
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16131541 B.Chan, G.Greenan, F.McKeon, and T.Ellenberger (2005).
Identification of a peptide fragment of DSCR1 that competitively inhibits calcineurin activity in vitro and in vivo.
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15997345 B.Scheller, A.Grandt, S.Wnendt, G.Lorenz, M.Böhm, and G.Nickenig (2005).
Comparative study of tacrolimus and paclitaxel stent coating in the porcine coronary model.
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16096803 E.G.Funhoff, T.E.de Jongh, and B.A.Averill (2005).
Direct observation of multiple protonation states in recombinant human purple acid phosphatase.
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15955057 E.G.Funhoff, Y.Wang, G.Andersson, and B.A.Averill (2005).
Substrate positioning by His92 is important in catalysis by purple acid phosphatase.
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Studies of the anticancer effect of calcineurin B.
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15625111 G.Schenk, L.R.Gahan, L.E.Carrington, N.Mitic, M.Valizadeh, S.E.Hamilton, J.de Jersey, and L.W.Guddat (2005).
Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase.
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PDB code: 1xzw
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Structural and biochemical characterization of CIB1 delineates a new family of EF-hand-containing proteins.
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PDB code: 1xo5
16059672 I.A.Doytchinova, V.Walshe, P.Borrow, and D.R.Flower (2005).
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La3+ stimulate the activity of calcineurin in two different ways.
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16113294 J.R.Blankenship, and J.Heitman (2005).
Calcineurin is required for Candida albicans to survive calcium stress in serum.
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15613384 J.R.Bradford, and D.R.Westhead (2005).
Improved prediction of protein-protein binding sites using a support vector machines approach.
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16466025 J.R.Carney, G.W.Ashley, R.L.Arslanian, and G.O.Buchannan (2005).
Structure elucidation of new ascomycins produced by genetic engineering.
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15994335 J.Y.Kim, and D.Saffen (2005).
Activation of M1 muscarinic acetylcholine receptors stimulates the formation of a multiprotein complex centered on TRPC6 channels.
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15577939 J.Yang, S.M.Roe, M.J.Cliff, M.A.Williams, J.E.Ladbury, P.T.Cohen, and D.Barford (2005).
Molecular basis for TPR domain-mediated regulation of protein phosphatase 5.
  EMBO J, 24, 1.
PDB code: 1wao
15670209 K.Hamada, M.Kato, T.Shimizu, K.Ihara, T.Mizuno, and T.Hakoshima (2005).
Crystal structure of the protein histidine phosphatase SixA in the multistep His-Asp phosphorelay.
  Genes Cells, 10, 1.
PDB codes: 1ujb 1ujc
16148011 S.Kang, H.Li, A.Rao, and P.G.Hogan (2005).
Inhibition of the calcineurin-NFAT interaction by small organic molecules reflects binding at an allosteric site.
  J Biol Chem, 280, 37698-37706.  
15987692 Y.Naoe, K.Arita, H.Hashimoto, H.Kanazawa, M.Sato, and T.Shimizu (2005).
Structural characterization of calcineurin B homologous protein 1.
  J Biol Chem, 280, 32372-32378.
PDB code: 2ct9
15749159 Y.Pommier, and J.Cherfils (2005).
Interfacial inhibition of macromolecular interactions: nature's paradigm for drug discovery.
  Trends Pharmacol Sci, 26, 138-145.  
15746091 Z.Z.Wu, S.R.Chen, and H.L.Pan (2005).
Transient receptor potential vanilloid type 1 activation down-regulates voltage-gated calcium channels through calcium-dependent calcineurin in sensory neurons.
  J Biol Chem, 280, 18142-18151.  
15155727 A.M.Weljie, and H.J.Vogel (2004).
Unexpected structure of the Ca2+-regulatory region from soybean calcium-dependent protein kinase-alpha.
  J Biol Chem, 279, 35494-35502.
PDB code: 1s6i
14691234 D.R.Caffrey, S.Somaroo, J.D.Hughes, J.Mintseris, and E.S.Huang (2004).
Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
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Structural and functional analysis of Mre11-3.
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Crystal structure of a myristoylated CAP-23/NAP-22 N-terminal domain complexed with Ca2+/calmodulin.
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Structural basis for the catalytic activity of human serine/threonine protein phosphatase-5.
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Molecular targeted treatments for fungal infections: the role of drug combinations.
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The crystal structure of the novel calcium-binding protein AtCBL2 from Arabidopsis thaliana.
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PDB code: 1mf8
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The role of calcium-binding proteins in the control of transcription: structure to function.
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PDB code: 1m63
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Calcineurin regulatory subunit is essential for virulence and mediates interactions with FKBP12-FK506 in Cryptococcus neoformans.
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Peptide interactions with G-protein coupled receptors.
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Potent inhibition of NFAT activation and T cell cytokine production by novel low molecular weight pyrazole compounds.
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11535607 J.T.Maynes, K.S.Bateman, M.M.Cherney, A.K.Das, H.A.Luu, C.F.Holmes, and M.N.James (2001).
Crystal structure of the tumor-promoter okadaic acid bound to protein phosphatase-1.
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PDB code: 1jk7
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Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase.
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PDB codes: 1ii7 1ii8
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Reversible inhibition of calcineurin by the polyphenolic aldehyde gossypol.
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11248035 T.Watanabe, H.B.Huang, A.Horiuchi, E.F.da Cruze Silva, L.Hsieh-Wilson, P.B.Allen, S.Shenolikar, P.Greengard, and A.C.Nairn (2001).
Protein phosphatase 1 regulation by inhibitors and targeting subunits.
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The NAF domain defines a novel protein-protein interaction module conserved in Ca2+-regulated kinases.
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Neuroimmunophilins: novel neuroprotective and neuroregenerative targets.
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Calcineurin activity is regulated both by redox compounds and by mutant familial amyotrophic lateral sclerosis-superoxide dismutase.
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Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics.
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PDB code: 1f40
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Modulation of the phosphatase activity of calcineurin by oxidants and antioxidants in vitro.
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10819596 E.Kimura (2000).
Dimetallic hydrolases and their models.
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Delineation of the calcineurin-interacting region of cyclophilin B.
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Immunophilins: switched on protein binding domains?
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Structures of the platelet calcium- and integrin-binding protein and the alphaIIb-integrin cytoplasmic domain suggest a mechanism for calcium-regulated recognition; homology modelling and NMR studies.
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Effect of vanadyl ions on calcineurin and its A subunit.
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The role of calcineurin in lymphocyte activation.
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A second calcineurin binding site on the NFAT regulatory domain.
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Enhancement of phototransduction protein interactions by lipid surfaces.
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Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes.
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Identification of a novel region critical for calcineurin function in vivo and in vitro.
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Comparison of the reaction progress of calcineurin with Mn2+ and Mg2+.
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Calcineurin. Structure, function, and inhibition.
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Study of FK-binding protein: FK506-metabolite complexes by electrospray mass spectrometry: correlation to immunosuppressive activity.
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Interaction of bacteriophage lambda protein phosphatase with Mn(II): evidence for the formation of a [Mn(II)]2 cluster.
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Three amino acid residues determine selective binding of FK506-binding protein 12.6 to the cardiac ryanodine receptor.
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Tartrate-resistant bone acid phosphatase: large-scale production and purification of the recombinant enzyme, characterization, and crystallization.
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Functional roles for fatty acylated amino-terminal domains in subcellular localization.
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Heterogeneous N-terminal acylation of retinal proteins.
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Genes for calcineurin B-like proteins in Arabidopsis are differentially regulated by stress signals.
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Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution.
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Stimulation of Elk1 transcriptional activity by mitogen-activated protein kinases is negatively regulated by protein phosphatase 2B (calcineurin).
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Calcium binding induces interaction between the N- and C-terminal domains of yeast calmodulin and modulates its overall conformation.
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Signaling through calcium, calcineurin, and NF-AT in lymphocyte activation and development.
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Bastadin 10 stabilizes the open conformation of the ryanodine-sensitive Ca(2+) channel in an FKBP12-dependent manner.
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High activity of the calcineurin A subunit with a V314 deletion.
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Characterization of calcineurin in human neutrophils. Inhibitory effect of hydrogen peroxide on its enzyme activity and on NF-kappaB DNA binding.
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Antifungal activities of antineoplastic agents: Saccharomyces cerevisiae as a model system to study drug action.
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Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12.
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Potential role of calcineurin for brain ischemia and traumatic injury.
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Autoantibodies to FK506 binding protein 12 (FKBP12) in autoimmune diseases.
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Affinity modulation of small-molecule ligands by borrowing endogenous protein surfaces.
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The therapeutic prescription for the organ transplant recipient: the linkage of immunosuppression and antimicrobial strategies.
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X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.
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PDB codes: 1bmi 2bmi
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AKAP79 inhibits calcineurin through a site distinct from the immunophilin-binding region.
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Inhibition of calcineurin by the tyrphostin class of tyrosine kinase inhibitors.
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Regulation of the calmodulin-stimulated protein phosphatase, calcineurin.
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