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Yorodumi- PDB-1cmk: CRYSTAL STRUCTURES OF THE MYRISTYLATED CATALYTIC SUBUNIT OF CAMP-... -
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-Basic information
Entry | Database: PDB / ID: 1cmk | ||||||
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Title | CRYSTAL STRUCTURES OF THE MYRISTYLATED CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE REVEAL OPEN AND CLOSED CONFORMATIONS | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHOTRANSFERASE / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information negative regulation of meiotic cell cycle process involved in oocyte maturation / CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling ...negative regulation of meiotic cell cycle process involved in oocyte maturation / CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / negative regulation of cAMP-dependent protein kinase activity / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / germinal vesicle / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / Vasopressin regulates renal water homeostasis via Aquaporins / negative regulation of protein import into nucleus / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Zheng, J. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. / Ten Eyck, L.F. | ||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Authors: Zheng, J. / Knighton, D.R. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M. / Ten Eyck, L.F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: The Crystal Structure of the Mammalian Catalytic Subunit of Camp-Dependent Protein Kinase and a Di-Iodinated Pki(5-24) Inhibitor Peptide Displays an Open Conformation Authors: Karlsson, R. / Zheng, J. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: 2.2 Angstroms Refined Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with Mnatp and a Peptide Inhibitor Authors: Zheng, J. / Trafny, E.A. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Ten Eyck, L.F. / Sowadski, J.M. #3: Journal: Biochemistry / Year: 1993 Title: Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with Mgatp and Peptide Inhibitor Authors: Zheng, J. / Knighton, D.R. / Ten Eyck, L.F. / Karlsson, R. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #4: Journal: Science / Year: 1991 Title: Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J. / Ten Eyck, L.F. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #5: Journal: Science / Year: 1991 Title: Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Authors: Knighton, D.R. / Zheng, J. / Ten Eyck, L.F. / Ashford, V.A. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M. #6: Journal: J.Biol.Chem. / Year: 1989 Title: Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli Authors: Slice, L.W. / Taylor, S.S. #7: Journal: J.Biol.Chem. / Year: 1981 Title: Differential Labeling and Identification of the Cysteine-Containing Tryptic Peptides of Catalytic Subunit from Porcine Heart Camp-Dependent Protein Kinase Authors: Nelson, N.C. / Taylor, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cmk.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cmk.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/1cmk ftp://data.pdbj.org/pub/pdb/validation_reports/cm/1cmk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: PHE E 327 - ASP E 328 OMEGA = 142.09 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ILE I 18 - HIS I 19 OMEGA = 114.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: HIS I 19 - ASP I 20 OMEGA = 138.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: THE MODEL HAS 2 COVALENTLY BOUND PHOSPHATES, ON THR 197, AND SER 338. THESE PHOSPHATES HAVE BEEN IDENTIFIED AS RESIDUES PO4 382 AND PO4 383. |
-Components
#1: Protein | Mass: 40705.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: HEART References: UniProt: P00517, UniProt: P36887*PLUS, cAMP-dependent protein kinase | ||||
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#2: Protein/peptide | Mass: 2452.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925 | ||||
#3: Chemical | #4: Chemical | Sequence details | SEQUENCE ADVISORY NOTICE THE SEQUENCE OF THE MAMMALIAN CA-SUBUNIT PRESENTED IN THIS ENTRY DIFFERS ...SEQUENCE ADVISORY NOTICE THE SEQUENCE OF THE MAMMALIAN CA-SUBUNIT PRESENTED IN THIS ENTRY DIFFERS FROM THE MOUSE RECOMBINAN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.85 Å3/Da / Density % sol: 74.62 % |
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Crystal grow | *PLUS Method: other / Details: Knighton, D.R., (1991) J. Mol. Biol., 220, 217. |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.9 Å / Num. obs: 20940 / Rmerge(I) obs: 0.097 |
-Processing
Software |
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Refinement | Resolution: 2.9→10 Å / Rfactor Rwork: 0.233 / Rfactor obs: 0.233 / σ(F): 2 Details: THE MAMMALIAN BINARY COMPLEX ADOPTED A DIFFERENT CONFORMATION THAN THE RECOMBINANT BINARY COMPLEX, PROTEIN DATA BANK ENTRY 2CPK. HOWEVER, MOST CONFORMATION CHANGES HAPPENED AT THE INTERFACE ...Details: THE MAMMALIAN BINARY COMPLEX ADOPTED A DIFFERENT CONFORMATION THAN THE RECOMBINANT BINARY COMPLEX, PROTEIN DATA BANK ENTRY 2CPK. HOWEVER, MOST CONFORMATION CHANGES HAPPENED AT THE INTERFACE BETWEEN TWO LOBES. THE SECONDARY STRUCTURE ASSIGNMENTS ARE THE SAME FOR EACH DOMAIN EXCEPT THE A HELIX, WHICH EXTENDS THREE MORE TURNS DUE TO THE STABILIZATION OF THE MYRISTYL GROUP. THIS MAKES THE ELECTRON DENSITY MORE VISIBLE IN THIS REGION. THE REGION BETWEEN RESIDUES 320 - 330 HAS POOR ELECTRON DENSITY. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: V2.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_bond_d / Dev ideal: 0.012 |