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- PDB-3hyh: Crystal structure of the protein kinase domain of yeast AMP-activ... -

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Basic information

Entry
Database: PDB / ID: 3hyh
TitleCrystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1
ComponentsCarbon catabolite-derepressing protein kinase
KeywordsTRANSFERASE / Kinase domain / ATP-binding / Carbohydrate metabolism / Kinase / Membrane / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / molecular function activator activity / nuclear membrane / non-specific serine/threonine protein kinase / negative regulation of translation / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / 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
Carbon catabolite-derepressing protein kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRudolph, M.J. / Amodeo, G.A. / Bai, Y. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1
Authors: Rudolph, M.J. / Amodeo, G.A. / Bai, Y. / Tong, L.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionJun 30, 2009ID: 3FAM
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: Carbon catabolite-derepressing protein kinase
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)62,6952
Polymers62,6952
Non-polymers00
Water1,928107
1
A: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)31,3471
Polymers31,3471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)31,3471
Polymers31,3471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.028, 75.137, 113.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASP / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 48 - 315 / Label seq-ID: 8 - 275

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carbon catabolite-derepressing protein kinase


Mass: 31347.488 Da / Num. of mol.: 2 / Fragment: Kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CAT1, CCR1, D8035.20, GLC2, PAS14, SNF1, YDR477W / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris (pH 8.5), 25% (w/v) PEG3350, and 300 mM (NH4)2SO4, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNumber: 36275
ReflectionResolution: 2.2→30 Å / Num. all: 42125 / Num. obs: 31518 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.2→2.256 Å / Redundancy: 2 % / Rmerge(I) obs: 0.605 / % possible all: 99

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.73 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.431 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1570 5 %RANDOM
Rwork0.23913 ---
obs0.24114 29853 99.7 %-
all-29855 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---0.2 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 0 107 3958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9745299
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32623.799179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5315744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4391526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022870
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21759
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22642
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.52455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07323820
X-RAY DIFFRACTIONr_scbond_it1.56231695
X-RAY DIFFRACTIONr_scangle_it2.3774.51479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A1865X-RAY DIFFRACTIONLOOSE POSITIONAL
11A1865X-RAY DIFFRACTIONLOOSE THERMAL
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 111 -
Rwork0.244 2123 -
obs--99.47 %
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)
13.57951.3943-1.47822.6166-0.8213.0679-0.1976-0.2021-0.4769-0.10340.0369-0.0580.0709-0.65160.1607-0.22920.00170.03910.07190.0196-0.047841.680233.939161.5094
24.13010.58642.65270.56830.66764.0468-0.40190.2667-0.05-0.14310.1266-0.0543-0.58080.17930.2753-0.0028-0.0352-0.0454-0.14950.0353-0.123562.097147.53953.5342
34.6282-1.056-2.00270.60530.73473.0452-0.16840.3866-0.47220.0707-0.0765-0.15810.22860.33590.2449-0.2328-0.03950.07450.0534-0.02340.078891.248930.83672.0716
42.0409-0.2164-0.09181.2655-0.48762.0935-0.0309-0.05110.00020.0698-0.0481-0.0824-0.1548-0.08210.079-0.0297-0.007-0.019-0.13730.0137-0.077670.553438.858685.6162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B54 - 135
2X-RAY DIFFRACTION2B136 - 315
3X-RAY DIFFRACTION3A54 - 135
4X-RAY DIFFRACTION4A136 - 315

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