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- PDB-1fmo: CRYSTAL STRUCTURE OF A POLYHISTIDINE-TAGGED RECOMBINANT CATALYTIC... -

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Entry
Database: PDB / ID: 1fmo
TitleCRYSTAL STRUCTURE OF A POLYHISTIDINE-TAGGED RECOMBINANT CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE COMPLEXED WITH THE PEPTIDE INHIBITOR PKI(5-24) AND ADENOSINE
Components
  • CAMP-DEPENDENT PROTEIN KINASEProtein kinase A
  • HEAT STABLE RABBIT SKELETAL MUSCLE INHIBITOR PROTEIN
KeywordsCOMPLEX (PHOSPHOTRANSFERASE/INHIBITOR) / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) / PHOSPHORYLATION / POLYHISTIDINE-TAG / PROTEIN KINASE / COMPLEX (PHOSPHOTRANSFERASE-INHIBITOR) complex
Function / homology
Function and homology information


spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion ...spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / negative regulation of cAMP-dependent protein kinase activity / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of protein import into nucleus / postsynaptic modulation of chemical synaptic transmission / molecular function inhibitor activity / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / protein kinase A catalytic subunit binding / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / regulation of G2/M transition of mitotic cell cycle / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / molecular adaptor activity / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion / nucleoplasm
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
ADENOSINE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.2 Å
AuthorsNarayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N.-H.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of a polyhistidine-tagged recombinant catalytic subunit of cAMP-dependent protein kinase complexed with the peptide inhibitor PKI(5-24) and adenosine.
Authors: Narayana, N. / Cox, S. / Shaltiel, S. / Taylor, S.S. / Xuong, N.
#1: Journal: Structure / Year: 1997
Title: A Binary Complex of the Catalytic Subunit of Camp-Dependent Protein Kinase and Adenosine Further Defines Conformational Flexibility
Authors: Narayana, N. / Cox, S. / Xuong, N.H. / Ten Eyck, L.F. / Taylor, S.S.
#2: 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.
#3: Journal: Protein Eng. / Year: 1993
Title: Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli: Multiple Isozymes Reflect Different Phosphorylation States
Authors: Herberg, F.W. / Bell, S.M. / Taylor, S.S.
#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.H. / Ten Eyck, L.F. / 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.H. / Ten Eyck, L.F. / Xuong, N.H. / Taylor, S.S. / Sowadski, J.M.
History
DepositionJul 8, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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: CAMP-DEPENDENT PROTEIN KINASE
I: HEAT STABLE RABBIT SKELETAL MUSCLE INHIBITOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1513
Polymers42,8842
Non-polymers2671
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-2 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.080, 78.440, 80.490
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 CAMP-DEPENDENT PROTEIN KINASE / Protein kinase A / CAPK / PKA


Mass: 40657.316 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: SKELETALSkeleton / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, EC: 2.7.1.37
#2: Protein/peptide HEAT STABLE RABBIT SKELETAL MUSCLE INHIBITOR PROTEIN / PKI-ALPHA / PKI(5-24)


Mass: 2226.411 Da / Num. of mol.: 1 / Fragment: RESIDUES 5 - 24
Source method: isolated from a genetically manipulated source
References: UniProt: P61926
#3: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4- ...Details: ORTHORHOMBIC CRYSTALS OF THE TERNARY COMPLEX, COMPRISED OF MOUSE HIS6-RC SUBUNIT, PKI (5-24) AND ADENOSINE, WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD USING 2-METHYL-2,4-PENTANEDIOL (MPD) AS THE PRECIPITATING AGENT. THE MOTHER-LIQUOR CONTAINED PROTEIN AT A CONCENTRATION OF 0.25 MM IN 100 MM BICINE BUFFER AT PH 8.0, 0.75 MM PKI(5-24), 4 MM ADENOSINE AND 4% MPD. THE RESERVOIR SOLUTION WAS MADE UP OF 20% MPD IN 100 MM BICINE BUFFER (PH 8.0). X-RAY DIFFRACTION QUALITY CRYSTALS (0.2 X 0.15 X 0.8 MM3) WERE GROWN AT 4 C IN APPROXIMATELY 4 - 6 WEEKS., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.25 mMprotein1drop
2100 mMBicine1drop
30.75 mMPKI(5-24)1drop
44 mMadenosine1drop
54 %MPD1drop
620 %MPD1reservoir
7100 mMBicine1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Feb 7, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 21679 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.064 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1 / Rsym value: 0.25 / % possible all: 84
Reflection
*PLUS
Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
TNT5Erefinement
X-PLOR3.1refinement
UCSDdata reduction
UCSDdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1APM

1apm


Resolution: 2.2→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.182 --
obs-19980 85 %
Solvent computationBsol: 167.1 Å2 / ksol: 0.45 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 19 90 3058
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01230441.3
X-RAY DIFFRACTIONt_angle_deg2.540882.8
X-RAY DIFFRACTIONt_dihedral_angle_d217860
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01782.2
X-RAY DIFFRACTIONt_gen_planes0.0143110
X-RAY DIFFRACTIONt_it3058
X-RAY DIFFRACTIONt_nbd0.041418
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20
X-RAY DIFFRACTIONt_plane_restr0.0110

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