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- PDB-6xqk: Crystal structure of the D/D domain of PKA from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6xqk
TitleCrystal structure of the D/D domain of PKA from S. cerevisiae
ComponentscAMP-dependent protein kinase regulatory subunit
KeywordsSIGNALING PROTEIN / Protein kinase A
Function / homology
Function and homology information


GPER1 signaling / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / protein localization to bud neck / Factors involved in megakaryocyte development and platelet production / regulation of cytoplasmic mRNA processing body assembly ...GPER1 signaling / PKA activation / PKA activation in glucagon signalling / DARPP-32 events / Vasopressin regulates renal water homeostasis via Aquaporins / CREB1 phosphorylation through the activation of Adenylate Cyclase / Hedgehog 'off' state / protein localization to bud neck / Factors involved in megakaryocyte development and platelet production / regulation of cytoplasmic mRNA processing body assembly / negative regulation of Ras protein signal transduction / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / regulation of protein phosphorylation / chromatin / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
cAMP-dependent protein kinase regulatory subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / molecular replacement / Resolution: 2.56 Å
AuthorsLarrieux, N. / Gonzalez Bardeci, N. / Trajtenberg, F. / Buschiazzo, A.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization.
Authors: Bardeci, N.G. / Tofolon, E. / Trajtenberg, F. / Caramelo, J. / Larrieux, N. / Rossi, S. / Buschiazzo, A. / Moreno, S.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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 regulatory subunit
B: cAMP-dependent protein kinase regulatory subunit
C: cAMP-dependent protein kinase regulatory subunit
D: cAMP-dependent protein kinase regulatory subunit
E: cAMP-dependent protein kinase regulatory subunit
F: cAMP-dependent protein kinase regulatory subunit
G: cAMP-dependent protein kinase regulatory subunit
H: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,57713
Polymers47,1738
Non-polymers4045
Water2,126118
1
A: cAMP-dependent protein kinase regulatory subunit
B: cAMP-dependent protein kinase regulatory subunit
C: cAMP-dependent protein kinase regulatory subunit
D: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7716
Polymers23,5864
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: cAMP-dependent protein kinase regulatory subunit
F: cAMP-dependent protein kinase regulatory subunit
G: cAMP-dependent protein kinase regulatory subunit
H: cAMP-dependent protein kinase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8067
Polymers23,5864
Non-polymers2203
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.824, 52.134, 68.832
Angle α, β, γ (deg.)90.000, 109.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
cAMP-dependent protein kinase regulatory subunit / cAPK regulatory subunit / Bypass of cyclase mutations protein 1 / Protein kinase A regulatory ...cAPK regulatory subunit / Bypass of cyclase mutations protein 1 / Protein kinase A regulatory subunit / PKA regulatory subunit


Mass: 5896.602 Da / Num. of mol.: 8 / Fragment: D/D domain (UNP residues 1-50)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BCY1, REG1, SRA1, YIL033C / Production host: Escherichia coli (E. coli) / References: UniProt: P07278
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% w/v PEG4000, 0.1 M Tris, pH 8.5, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 108 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 27, 2013 / Details: Varimax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.557→64.8 Å / Num. obs: 12426 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 42.81 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 12
Reflection shellResolution: 2.56→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Num. unique obs: 1777 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (20-MAY-2020)refinement
XDSdata reduction
Aimless0.1.29data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.56→64.8 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.818 / SU R Cruickshank DPI: 1.898 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.386 / SU Rfree Blow DPI: 0.336 / SU Rfree Cruickshank DPI: 0.341
RfactorNum. reflection% reflectionSelection details
Rfree0.27 601 4.84 %RANDOM
Rwork0.214 ---
obs0.217 12414 99.6 %-
Displacement parametersBiso max: 73.64 Å2 / Biso mean: 30.81 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1--5.9042 Å20 Å2-3.7839 Å2
2--5.071 Å20 Å2
3---0.8333 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.56→64.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 25 118 3034
Biso mean--32.45 21.56 -
Num. residues----355
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1058SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes536HARMONIC5
X-RAY DIFFRACTIONt_it2973HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion364SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2602SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2973HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3991HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion16.41
LS refinement shellResolution: 2.56→2.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.2569 17 4.11 %
Rwork0.2183 397 -
all0.2197 414 -
obs--97.84 %
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)
1-0.4325-0.91420.66151.6098-0.1690.6192-0.038-0.01480.0447-0.06670.1292-0.20430.08170.1188-0.0912-0.0596-0.01160.0121-0.0582-0.0490.031823.516118.292919.3827
20.6352-0.0387-0.77311.9887-0.1142-0.6352-0.0804-0.07-0.1137-0.19760.1716-0.1921-0.21390.0192-0.09120.0296-0.06460.0265-0.0566-0.0563-0.034424.757830.445517.0041
30.390.8112-1.55860.5391.12055.66360.00760.1713-0.09750.17910.1730.2834-0.5151-0.5981-0.1806-0.06570.08710.01310.00380.0054-0.03023.549226.429715.7117
4-0.0293-0.0711-0.73440.17560.79825.7603-0.01550.2815-0.3146-0.7575-0.0053-0.04510.339-0.50920.02080.0606-0.0339-0.0653-0.0336-0.0458-0.07327.708521.98185.0792
50.75190.8915-0.18193.128-2.04190.3148-0.1780.016-0.2658-0.2468-0.03780.08310.3553-0.22830.21580.0186-0.04310.0367-0.1009-0.0547-0.042620.480244.157315.7244
61.7177-0.8913-0.18510.3829-1.0161-0.1547-0.0770.09550.14620.0833-0.01310.012-0.1118-0.0920.09010.0152-0.0391-0.0285-0.09130.0007-0.025320.167655.796418.2469
71.48150.5548-0.58710-0.16562.9223-0.1147-0.3597-0.10290.34470.1066-0.21880.57380.6090.0081-0.00130.1282-0.0310.00640.0276-0.022139.473848.387526.2506
82.8229-1.2753-0.574201.70854.0566-0.2309-0.04230.3825-0.5288-0.0136-0.2752-0.15550.76950.2445-0.0495-0.01820.1082-0.00840.10230.020741.816351.694314.7281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }0
2X-RAY DIFFRACTION2{ B|* }0
3X-RAY DIFFRACTION3{ C|* }0
4X-RAY DIFFRACTION4{ D|* }0
5X-RAY DIFFRACTION5{ E|* }0
6X-RAY DIFFRACTION6{ F|* }0
7X-RAY DIFFRACTION7{ G|* }0
8X-RAY DIFFRACTION8{ H|* }0

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