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- PDB-5ot3: Crystal Structure of the Protein-Kinase A catalytic subunit from ... -

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Basic information

Entry
Database: PDB / ID: 5ot3
TitleCrystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in complex with compounds RKp191 and RKp117
Components(cAMP-dependent protein kinase ...) x 2
KeywordsTRANSFERASE / Complex / peptidic ligand
Function / homology
Function and homology information


negative regulation of cAMP/PKA signal transduction / 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 ...negative regulation of cAMP/PKA signal transduction / 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 / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / 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 / mRNA processing / adenylate cyclase-activating G protein-coupled receptor signaling pathway / manganese ion binding / cellular response to heat / 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 / mitochondrion / ATP binding / nucleus / 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
Chem-9LQ / beta-D-ribopyranose / cAMP-dependent protein kinase inhibitor / UPF0418 protein FAM164A / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMueller, J.M. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Loewe Corporation Germany
CitationJournal: Acs Omega / Year: 2019
Title: Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
Authors: Mueller, J.M. / Kirschner, R. / Geyer, A. / Klebe, G.
History
DepositionAug 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cAMP-dependent protein kinase catalytic subunit alpha
D: cAMP-dependent protein kinase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9126
Polymers43,1832
Non-polymers7294
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-20 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.210, 72.752, 76.925
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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CAMP-dependent protein kinase ... , 2 types, 2 molecules AD

#1: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 41193.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Tissue: Ovary / Gene: PRKACA / Organ: Ovary / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: P25321, cAMP-dependent protein kinase
#2: Protein/peptide cAMP-dependent protein kinase inhibitor


Mass: 1989.177 Da / Num. of mol.: 1 / Fragment: UNP Residues 6-23 / Source method: obtained synthetically
Details: cAMP-dependent protein kinase inhibitor with A17RBS mutation
Source: (synth.) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A061IH64, UniProt: G3HK48*PLUS

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-9LQ / [2-[(4-isoquinolin-5-ylsulfonyl-1,4-diazepan-1-yl)methyl]phenyl]boronic acid


Mass: 425.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24BN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 100 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 5 mM RKp117, 20 % v/v methanol/water in reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.886 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.04→42.007 Å / Num. obs: 25374 / % possible obs: 99.9 % / Redundancy: 7.63 % / CC1/2: 0.999 / Rsym value: 0.06 / Net I/σ(I): 20.68
Reflection shellResolution: 2.04→2.16 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 3.86 / Num. unique obs: 4008 / CC1/2: 0.912 / Rsym value: 0.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→42.007 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1269 5 %Random selection
Rwork0.1837 ---
obs0.1859 25371 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→42.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 45 92 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072917
X-RAY DIFFRACTIONf_angle_d0.8363967
X-RAY DIFFRACTIONf_dihedral_angle_d16.3721710
X-RAY DIFFRACTIONf_chiral_restr0.053425
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0388-2.12050.30251370.21572603X-RAY DIFFRACTION99
2.1205-2.2170.31881390.19812635X-RAY DIFFRACTION100
2.217-2.33380.2251390.19352654X-RAY DIFFRACTION100
2.3338-2.48010.25681400.19792653X-RAY DIFFRACTION100
2.4801-2.67150.29221390.20942641X-RAY DIFFRACTION100
2.6715-2.94030.27251410.2232679X-RAY DIFFRACTION100
2.9403-3.36560.24821410.20552678X-RAY DIFFRACTION100
3.3656-4.23970.19861430.1632726X-RAY DIFFRACTION100
4.2397-42.01630.17821500.15762833X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2432-0.29020.18860.3357-0.22240.1360.01170.31650.2698-0.08360.09560.3955-0.17330.002300.34080.01240.02890.4412-0.03490.333911.524915.7758-3.9842
20.36770.45610.12930.53880.13740.08040.01590.11980.0321-0.1492-0.02270.08560.0085-0.0929-0.00010.22360.0205-0.0210.3556-0.04950.27489.215813.9916-2.4757
30.1632-0.2269-0.05930.1057-0.05870.7962-0.0120.0854-0.08680.00530.01230.08310.04410.097900.22530.0008-0.01240.2710.01140.251512.095116.3712.8299
40.96020.38930.01270.8641-0.32330.105-0.0069-0.08530.0562-0.0724-0.02510.2309-0.04580.08190.00050.2640.03080.01770.1782-0.00330.24383.610319.757522.9167
50.3813-0.00820.42370.1685-0.00450.5389-0.049-0.53390.09440.58990.0126-0.0225-0.14820.1455-0.00160.3655-0.01050.04230.3345-0.01260.22489.893318.185636.727
60.18550.0804-0.37880.43460.26361.02560.0380.1175-0.148-0.16110.00390.15450.10830.0258-00.2072-0.0325-0.00750.25890.01960.33112.209212.40837.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 252 )
5X-RAY DIFFRACTION5chain 'A' and (resid 253 through 297 )
6X-RAY DIFFRACTION6chain 'A' and (resid 298 through 350 )

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