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- PDB-4wb6: Crystal structure of a L205R mutant of human cAMP-dependent prote... -

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Basic information

Entry
Database: PDB / ID: 4wb6
TitleCrystal structure of a L205R mutant of human cAMP-dependent protein kinase A (catalytic alpha subunit)
Components
  • (cAMP-dependent protein kinase catalytic subunit ...) x 2
  • PKI (5-24)
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Cushing's syndrome / protein kinase / phosphorylation / mutant / adenosine triphosphate / catalysis / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / regulation of protein processing / Loss of phosphorylation of MECP2 at T308 / cAMP-dependent protein kinase activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / 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 interleukin-2 production / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / Triglyceride catabolism / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / cAMP/PKA signal transduction / PKA activation in glucagon signalling / mesoderm formation / RET signaling / Regulation of MECP2 expression and activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / sperm flagellum / plasma membrane raft / DARPP-32 events / regulation of cardiac muscle contraction / regulation of cardiac conduction / regulation of macroautophagy / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / renal water homeostasis / Hedgehog 'off' state / Ion homeostasis / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / regulation of G2/M transition of mitotic cell cycle / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / sperm midpiece / Recruitment of mitotic centrosome proteins and complexes / cellular response to epinephrine stimulus / calcium channel complex / negative regulation of smoothened signaling pathway / Mitochondrial protein degradation / Recruitment of NuMA to mitotic centrosomes / positive regulation of gluconeogenesis / Anchoring of the basal body to the plasma membrane / CD209 (DC-SIGN) signaling / cellular response to glucagon stimulus / protein serine/threonine/tyrosine kinase activity / positive regulation of calcium-mediated signaling / FCGR3A-mediated IL10 synthesis / regulation of heart rate / protein export from nucleus / AURKA Activation by TPX2 / acrosomal vesicle / positive regulation of protein export from nucleus / Regulation of insulin secretion / neural tube closure / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / cellular response to glucose stimulus / MAPK6/MAPK4 signaling / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / neuromuscular junction / positive regulation of insulin secretion / cytokine-mediated signaling pathway / VEGFA-VEGFR2 Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / Regulation of PLK1 Activity at G2/M Transition / GPER1 signaling / manganese ion binding / Factors involved in megakaryocyte development and platelet production / cellular response to heat / peptidyl-serine phosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells
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
ADENOSINE-5'-TRIPHOSPHATE / cAMP-dependent protein kinase catalytic subunit alpha / cAMP-dependent protein kinase inhibitor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural insights into mis-regulation of protein kinase A in human tumors.
Authors: Cheung, J. / Ginter, C. / Cassidy, M. / Franklin, M.C. / Rudolph, M.J. / Robine, N. / Darnell, R.B. / Hendrickson, W.A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_keywords.text
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,16710
Polymers86,0564
Non-polymers1,1126
Water3,549197
1
A: cAMP-dependent protein kinase catalytic subunit alpha
I: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5845
Polymers43,0282
Non-polymers5563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-24 kcal/mol
Surface area16210 Å2
MethodPISA
2
B: cAMP-dependent protein kinase catalytic subunit alpha
J: PKI (5-24)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5845
Polymers43,0282
Non-polymers5563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-26 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.169, 90.193, 90.377
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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CAMP-dependent protein kinase catalytic subunit ... , 2 types, 2 molecules AB

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


Mass: 40801.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Protein cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 40801.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKACA, PKACA / Production host: Escherichia coli (E. coli) / References: UniProt: P17612, cAMP-dependent protein kinase

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Protein/peptide , 1 types, 2 molecules IJ

#3: Protein/peptide PKI (5-24)


Mass: 2226.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61925*PLUS

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Non-polymers , 3 types, 203 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG 8000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 52562 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/av σ(I): 20.8 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.85 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WB8

4wb8


Resolution: 2.1→40.492 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 2572 4.94 %RANDOM
Rwork0.1878 ---
obs0.1903 52060 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→40.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 66 197 6203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086156
X-RAY DIFFRACTIONf_angle_d1.0578320
X-RAY DIFFRACTIONf_dihedral_angle_d14.9662302
X-RAY DIFFRACTIONf_chiral_restr0.044865
X-RAY DIFFRACTIONf_plane_restr0.0051052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13460.36261270.28162566X-RAY DIFFRACTION93
2.1346-2.17820.34111350.27862753X-RAY DIFFRACTION99
2.1782-2.22550.32971210.28332789X-RAY DIFFRACTION100
2.2255-2.27730.54651260.48392468X-RAY DIFFRACTION89
2.2773-2.33430.34191550.26442771X-RAY DIFFRACTION100
2.3343-2.39740.33051400.23072734X-RAY DIFFRACTION99
2.3974-2.46790.30411580.23432755X-RAY DIFFRACTION99
2.4679-2.54750.29721580.23262728X-RAY DIFFRACTION99
2.5475-2.63860.30881200.22722772X-RAY DIFFRACTION100
2.6386-2.74420.31321510.23732775X-RAY DIFFRACTION100
2.7442-2.86910.25281740.22142753X-RAY DIFFRACTION100
2.8691-3.02030.29021340.22262795X-RAY DIFFRACTION100
3.0203-3.20940.30461510.21092789X-RAY DIFFRACTION100
3.2094-3.45710.23061510.20882754X-RAY DIFFRACTION100
3.4571-3.80480.25231620.18252791X-RAY DIFFRACTION100
3.8048-4.35480.171550.14362788X-RAY DIFFRACTION100
4.3548-5.48440.16871220.12412825X-RAY DIFFRACTION100
5.4844-40.50.14041320.13292882X-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)
12.87430.9709-0.01533.4282-1.11074.4393-0.13940.0579-0.0661-0.10350.1471-0.5212-0.23710.70740.00080.395-0.03060.03550.4823-0.09440.33991.8356-17.6062-23.3619
21.51140.1563-0.36862.36350.50584.4214-0.08810.1167-0.1483-0.1170.0942-0.22390.13080.364-0.02290.2679-0.0210.00420.3546-0.05480.3714-4.0296-22.8688-31.8832
33.5844-0.1231-0.82051.44640.09399.4483-0.10990.3079-0.0639-0.30030.04210.2359-0.2319-1.43370.04750.4134-0.0409-0.00560.5023-0.07430.4062-19.2493-23.538-34.1244
43.57680.4685-0.44861.89810.03545.5672-0.28020.584-0.4735-0.46740.2670.08040.9509-0.46180.01250.7916-0.14110.03320.5008-0.14470.4808-12.9159-36.7777-41.7507
52.91430.2308-2.0015.81752.46162.9350.1386-0.01290.1473-0.41480.1379-0.3151-1.0640.9993-0.33260.5066-0.0442-0.03150.59660.01640.42920.2522-7.0667-27.8508
64.53620.2629-0.22683.4166-0.20334.54810.1604-0.1308-0.318-0.0901-0.14060.05870.6342-0.9606-0.03360.5192-0.0717-0.01220.51160.07010.3029-21.7296-34.08852.9681
72.30990.83430.69142.98670.04257.27290.0351-0.1124-0.16390.1182-0.046-0.00570.2432-1.16620.00060.3123-0.0070.01190.45420.02050.3352-23.5292-28.76016.7371
82.24130.57450.20992.4041-0.14225.91950.1023-0.32050.20710.2697-0.171-0.066-0.9502-0.02760.05780.55750.0089-0.02360.35350.03440.3439-11.612-18.958215.1544
93.19570.5061-0.05212.2848-0.89187.0767-0.0995-0.1879-0.0931-0.00540.11880.35670.3601-1.6044-0.00790.58320.00780.02780.9178-0.02860.5144-35.124-29.36343.1746
109.7731-0.64893.70732.43273.78398.208-0.41982.06680.1535-1.8772-0.97420.9155-0.9931-0.79981.29170.82520.0519-0.09711.0588-0.04550.5456-19.5859-15.7819-53.5762
115.00894.28583.41236.84021.35133.1682-0.0529-0.16830.56970.7932-0.42270.8832-1.3701-1.39250.53510.65010.07610.03340.6262-0.10060.532-14.8524-12.0254-39.5553
126.73580.7902-2.20293.182-2.58732.47621.3777-0.83981.01071.0295-0.20010.1453-1.76430.4483-1.04151.28560.15890.15971.1038-0.12620.6912-24.5271-8.763528.4152
135.6613-0.091-3.77284.46513.15535.45980.2672-0.42680.828-0.1372-0.38981.1798-2.0339-1.41490.08410.88390.3550.02610.8589-0.12060.6248-28.9227-12.619115.11
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 179 )
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 252 )
4X-RAY DIFFRACTION4chain 'A' and (resid 253 through 316 )
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 350 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 81 )
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 316 )
9X-RAY DIFFRACTION9chain 'B' and (resid 317 through 350 )
10X-RAY DIFFRACTION10chain 'I' and (resid 5 through 13 )
11X-RAY DIFFRACTION11chain 'I' and (resid 14 through 23 )
12X-RAY DIFFRACTION12chain 'J' and (resid 5 through 11 )
13X-RAY DIFFRACTION13chain 'J' and (resid 12 through 24 )

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