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- PDB-1cmk: CRYSTAL STRUCTURES OF THE MYRISTYLATED CATALYTIC SUBUNIT OF CAMP-... -

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Entry
Database: PDB / ID: 1cmk
TitleCRYSTAL STRUCTURES OF THE MYRISTYLATED CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE REVEAL OPEN AND CLOSED CONFORMATIONS
Components
  • cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT
  • cAMP-dependent protein kinase inhibitor, alpha form
KeywordsTRANSFERASE/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 / 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 / Factors involved in megakaryocyte development and platelet production / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / negative regulation of cAMP-dependent protein kinase activity / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction / germinal vesicle / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / cAMP-dependent protein kinase activity / protein localization to lipid droplet / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of protein import into nucleus / regulation of osteoblast differentiation / cellular response to cold / Mitochondrial protein degradation / sperm capacitation / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / intracellular potassium ion homeostasis / mesoderm formation / plasma membrane raft / axoneme / sperm flagellum / postsynaptic modulation of chemical synaptic transmission / regulation of G2/M transition of mitotic cell cycle / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / acrosomal vesicle / protein export from nucleus / positive regulation of phagocytosis / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / neural tube closure / neuromuscular junction / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / peptidyl-serine phosphorylation / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / protein phosphorylation / protein kinase activity / postsynapse / regulation of cell cycle / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase inhibitor / cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / MYRISTIC ACID / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsZheng, 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
DepositionNov 18, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2012Group: Source and taxonomy
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
E: cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT
I: cAMP-dependent protein kinase inhibitor, alpha form
E: MYRISTIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6405
Polymers43,1582
Non-polymers4823
Water00
1
E: cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT
I: cAMP-dependent protein kinase inhibitor, alpha form
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)261,84230
Polymers258,94912
Non-polymers2,89318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+3/4,-x+3/4,-z+3/41
crystal symmetry operation19_555-x+3/4,-z+3/4,-y+3/41
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
Unit cell
Length a, b, c (Å)171.520, 171.520, 171.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Atom site foot note1: 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.

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Components

#1: Protein cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT


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
#2: Protein/peptide cAMP-dependent protein kinase inhibitor, alpha form


Mass: 2452.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
Has protein modificationY
Sequence detailsSEQUENCE 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 RECOMBINANT C-SUBUNIT AT THE FOLLOWING POSITIONS: SWISS-PROT ENTRY NAME: KAPA_MOUSE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE THR 32 ASN E 32 SER 34 ALA E 34 GLN 39 HIS E 39 ASP 44 GLU E 44 SER 65 THR E 65 TYR 69 PHE E 69 PHE 108 TYR E 108 ALA 124 PRO E 124 ASN 286 ASP E 286 THR 348 SER E 348

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.62 %
Crystal grow
*PLUS
Method: other / Details: Knighton, D.R., (1991) J. Mol. Biol., 220, 217.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 20940 / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
X-PLOR2model building
X-PLOR2refinement
X-PLOR2phasing
RefinementResolution: 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 stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 17 0 3047
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: V2.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.012

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