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- PDB-1ctp: STRUCTURE OF THE MAMMALIAN CATALYTIC SUBUNIT OF CAMP-DEPENDENT PR... -

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Basic information

Entry
Database: PDB / ID: 1ctp
TitleSTRUCTURE OF THE MAMMALIAN CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE AND AN INHIBITOR PEPTIDE DISPLAYS AN OPEN CONFORMATION
Components
  • cAMP-DEPENDENT PROTEIN KINASE
  • cAMP-dependent protein kinase inhibitor, alpha form
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE(PHOSPHOTRANSFERASE) / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of meiotic cell cycle process involved in oocyte maturation / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / germinal vesicle / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / negative regulation of protein import into nucleus / molecular function inhibitor activity ...negative regulation of meiotic cell cycle process involved in oocyte maturation / negative regulation of cAMP-dependent protein kinase activity / negative regulation of cAMP/PKA signal transduction / germinal vesicle / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / negative regulation of protein import into nucleus / molecular function inhibitor activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / sperm flagellum / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / acrosomal vesicle / cellular response to heat / molecular adaptor activity / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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. / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
MYRISTIC ACID / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsKarlsson, R. / Zheng, J. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation.
Authors: Karlsson, R. / Zheng, J. / Xuong, N. / Taylor, S.S. / Sowadski, J.M.
#1: Journal: Biochemistry / Year: 1993
Title: Crystal-Structure of the Catalytic Subunit of Camp-Dependent Protein-Kinase Complexed with a Mgatp and Peptide Inhibitor
Authors: Zheng, J. / Knighton, D.R. / Xuong, N.-H. / Eyck, L.F.T. / Karlsson, R. / Taylor, S.S. / Sowadski, J.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: 2.0 Angstroms Refined Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase Complexed with a Peptide Inhibitor and Detergent
Authors: Knighton, D.R. / Bell, S.M. / Zheng, J. / Eyck, L.F.T. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#3: 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.H. / Trafny, E.A. / Knighton, D.R. / Xuong, N.-H. / Taylor, S.S. / Eyck, L.F.T. / Sowadski, J.M.
#4: Journal: Science / Year: 1991
Title: Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
Authors: Knighton, D.R. / Zheng, J. / Eyck, L.F.T. / Ashford, V.A. / Xuong, N.-H. / Taylor, S.S. / Sowadski, J.M.
#5: 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. / Eyck, L.F.T. / 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.
History
DepositionApr 8, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)43,3313
Polymers43,1032
Non-polymers2281
Water362
1
E: cAMP-DEPENDENT PROTEIN KINASE
I: cAMP-dependent protein kinase inhibitor, alpha form
hetero molecules

E: cAMP-DEPENDENT PROTEIN KINASE
I: cAMP-dependent protein kinase inhibitor, alpha form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6626
Polymers86,2054
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_545-x+1/4,z-1/4,y+1/41
Unit cell
Length a, b, c (Å)171.500, 171.500, 171.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Atom site foot note1: N-TERMINAL IS MYRISTOYLATED BUT ONLY THE LAST 10 ATOMS OF THE ALKANE CHAIN WERE LOCATED. THE MYRISTOYLATE GROUP IS PRESENTED ON *HETATM* RECORDS AT THE END OF THE CHAIN.
2: RESIDUE THR E 197 IS PHOSPHORYLATED.

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Components

#1: Protein cAMP-DEPENDENT PROTEIN KINASE


Mass: 40624.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P36887, EC: 2.7.1.37
#2: Protein/peptide cAMP-dependent protein kinase inhibitor, alpha form


Mass: 2478.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925, UniProt: P61926*PLUS
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsN-TERMINAL IS MYRISTOYLATED BUT ONLY THE LAST 10 ATOMS OF THE ALKANE CHAIN WERE LOCATED. THE ...N-TERMINAL IS MYRISTOYLATED BUT ONLY THE LAST 10 ATOMS OF THE ALKANE CHAIN WERE LOCATED. THE MYRISTOYLATE GROUP IS PRESENTED ON *HETATM* RECORDS AT THE END OF THE CHAIN. THERE ARE NINE MUTATIONS BETWEEN THE MOUSE RECOMBINANT FORM OF THE ENZYME (PDB ENTRY 2CPK) AND THE PORCINE ENZYME GIVEN IN THIS ENTRY. THE MUTATIONS ARE: PORCINE ENZYME - MOUSE RECOMBINANT ENZYME ASN 32 THR 32 ALA 34 SER 34 HIS 39 GLN 39 GLU 44 ASP 44 THR 65 SER 65 PHE 69 TYR 69 TYR 108 PHE 108 PRO 124 ALA 124 SER 348 THR 348
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.91 Å3/Da / Density % sol: 74.96 %
Crystal grow
*PLUS
Method: other / Details: Knighton, D.R., (1991) Science, 253, 414.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 17821 / Rmerge(I) obs: 0.097 / Num. measured all: 119740

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.9→7 Å / Rfactor obs: 0.19
Details: THE TEMPERATURE FACTOR OF OH TYR E 108 IS ABOUT 30 UNITS GREATER THAN THOSE OF THE ATOMS IN THE PHENYL RING.
Refinement stepCycle: LAST / Resolution: 2.9→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 10 2 2732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.022
X-RAY DIFFRACTIONt_angle_deg4.3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 7 Å / Num. reflection obs: 17077 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.2 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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