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- PDB-1yds: Structure of CAMP-dependent protein kinase, alpha-catalytic subun... -

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Basic information

Entry
Database: PDB / ID: 1yds
TitleStructure of CAMP-dependent protein kinase, alpha-catalytic subunit in complex with H8 protein kinase inhibitor [N-(2-methylamino)ethyl]-5-isoquinolinesulfonamide
Components
  • C-AMP-DEPENDENT PROTEIN KINASE
  • PROTEIN KINASE INHIBITOR PEPTIDE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PHOSPHOTRANSFERASE / TRANSFERASE / CAMP / PHOSPHORYLATION / ISOQUINOLINE SULFONAMIDE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


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 ...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 / Mitochondrial protein degradation / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / mesoderm formation / sperm flagellum / negative regulation of TORC1 signaling / protein kinase A 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 / 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
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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-IQS / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEngh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Crystal structures of catalytic subunit of cAMP-dependent protein kinase in complex with isoquinolinesulfonyl protein kinase inhibitors H7, H8, and H89. Structural implications for selectivity.
Authors: Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
#1: Journal: Embo J. / Year: 1993
Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ ...Title: Phosphotransferase and Substrate Binding Mechanism of the Camp-Dependent Protein Kinase Catalytic Subunit from Porcine Heart as Deduced from the 2.0 A Structure of the Complex with Mn2+ Adenylyl Imidodiphosphate and Inhibitor Peptide Pki(5-24)
Authors: Bossemeyer, D. / Engh, R.A. / Kinzel, V. / Ponstingl, H. / Huber, R.
#2: Journal: Biochim.Biophys.Acta / Year: 1992
Title: Cloning of the C Alpha Catalytic Subunit of the Bovine Camp-Dependent Protein Kinase
Authors: Wiemann, S. / Kinzel, V. / Pyerin, W.
#3: Journal: Biochemistry / Year: 1984
Title: Isoquinolinesulfonamides, Novel and Potent Inhibitors of Cyclic Nucleotide Dependent Protein Kinase and Protein Kinase C
Authors: Hidaka, H. / Inagaki, M. / Kawamoto, S. / Sasaki, Y.
History
DepositionJul 24, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Structure summary
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: C-AMP-DEPENDENT PROTEIN KINASE
I: PROTEIN KINASE INHIBITOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1733
Polymers42,9082
Non-polymers2651
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.380, 76.200, 80.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein C-AMP-DEPENDENT PROTEIN KINASE / CAPK / PKA C-ALPHA


Mass: 40681.363 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Details: ALPHA ISOENZYME / Source: (gene. exp.) Bos taurus (cattle) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P00517, EC: 2.7.1.37
#2: Protein/peptide PROTEIN KINASE INHIBITOR PEPTIDE / PKI / PKI-ALPHA


Mass: 2226.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P04541, UniProt: P63249*PLUS
#3: Chemical ChemComp-IQS / N-[2-(METHYLAMINO)ETHYL]-5-ISOQUINOLINESULFONAMIDE / H-8


Mass: 265.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % METHANOL, 70 MILLIMOLAR SODIUM SULFATE, 20 MILLIMOLAR MES-BIS-TRIS PH 6.5, 279K USING HANGING DROP DIFFUSION., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.6 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
225 mMMes-BisTris1drop
375 mM1dropLiCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
61.5 mMoctanoyl-N-methylglucamide1drop
71.5 mMH inhibitor1drop
81 mMPKI-(5-24)1drop
915 %methanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 17182 / % possible obs: 77 %
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.29 Å / % possible obs: 51 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementResolution: 2.2→6 Å / Rfactor Rwork: 0.199 / Rfactor obs: 0.199 / σ(F): 3
Details: ONLY THE WATER MOLECULES IN THE VICINITY OF THE BOUND H-8 INHIBITOR MOLECULE HAVE BEEN MODELED. THE PEPTIDE CHAIN IN THE REGION OF THE GLYCINE FLAP RESIDUES GLY E 50 TO VAL E 57 ADOPTS OPEN ...Details: ONLY THE WATER MOLECULES IN THE VICINITY OF THE BOUND H-8 INHIBITOR MOLECULE HAVE BEEN MODELED. THE PEPTIDE CHAIN IN THE REGION OF THE GLYCINE FLAP RESIDUES GLY E 50 TO VAL E 57 ADOPTS OPEN AND CLOSED CONFORMATIONS. INCLUDED ARE THE COORDINATES OF THE MODEL REFINED IN THE OPEN CONFORMATION.
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 18 21 2974
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.8

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