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- PDB-2h6d: Protein Kinase Domain of the Human 5'-AMP-activated protein kinas... -

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Basic information

Entry
Database: PDB / ID: 2h6d
TitleProtein Kinase Domain of the Human 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPK alpha-2 chain)
Components5'-AMP-activated protein kinase catalytic subunit alpha-2
KeywordsSIGNALING PROTEIN / TRANSFERASE / ATP-binding / Cholesterol biosynthesis / Fatty acid biosynthesis / Kinase / Lipid synthesis / Nucleotide-binding / Phosphorylation / Serine/threonine-protein kinase / Steroid biosynthesis / Sterol biosynthesis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / nucleotide-activated protein kinase complex ...[hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / : / regulation of stress granule assembly / histone H2BS36 kinase activity / AMPK inhibits chREBP transcriptional activation activity / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine metabolism / negative regulation of hepatocyte apoptotic process / protein localization to lipid droplet / negative regulation of TOR signaling / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / Macroautophagy / positive regulation of protein localization / cholesterol biosynthetic process / cellular response to nutrient levels / positive regulation of macroautophagy / regulation of macroautophagy / fatty acid homeostasis / cellular response to glucose starvation / positive regulation of autophagy / energy homeostasis / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / negative regulation of TORC1 signaling / cellular response to calcium ion / protein serine/threonine/tyrosine kinase activity / positive regulation of glycolytic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / TP53 Regulates Metabolic Genes / regulation of circadian rhythm / Wnt signaling pathway / fatty acid biosynthetic process / autophagy / cytoplasmic stress granule / cellular response to prostaglandin E stimulus / rhythmic process / cellular response to xenobiotic stimulus / glucose homeostasis / cellular response to oxidative stress / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / nuclear speck / axon / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / chromatin binding / dendrite / negative regulation of apoptotic process / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / 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 ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / 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
5'-AMP-activated protein kinase catalytic subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLittler, D.R. / Walker, J.R. / Wybenga-Groot, L. / Newman, E.M. / Butler-Cole, C. / Mackenzie, F. / Finerty, P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. ...Littler, D.R. / Walker, J.R. / Wybenga-Groot, L. / Newman, E.M. / Butler-Cole, C. / Mackenzie, F. / Finerty, P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation.
Authors: Littler, D.R. / Walker, J.R. / Davis, T. / Wybenga-Groot, L.E. / Finerty, P.J. / Newman, E. / Mackenzie, F. / Dhe-Paganon, S.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)31,5581
Polymers31,5581
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.454, 67.410, 50.493
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-2 / E.C.2.7.11.1 / AMPK alpha-2 chain


Mass: 31557.746 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P54646, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18.6% PEG 4000, 0.1M AmSO4, 0.1M Tris-HCl pH 8.5, 15%v/v isopropanol,5mM ATP/MgCl, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 19, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.72 Å / Num. all: 22387 / Num. obs: 22387 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.047 / Net I/σ(I): 26.91
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 930 / Rsym value: 0.504 / % possible all: 83

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-2000data reduction
PHASERphasing
RESOLVEmodel building
ARP/wARPmodel building
REFMAC5.2refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FH9

2fh9


Resolution: 1.85→19.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.413 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22674 1147 5.1 %RANDOM
Rwork0.18803 ---
obs0.19003 21209 98.76 %-
all-22636 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-0.57 Å2
2--0.64 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 164 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222116
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9632855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5015254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28722.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26615386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3641515
X-RAY DIFFRACTIONr_chiral_restr0.120.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021569
X-RAY DIFFRACTIONr_nbd_refined0.220.2975
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.214
X-RAY DIFFRACTIONr_mcbond_it1.99731317
X-RAY DIFFRACTIONr_mcangle_it2.72842060
X-RAY DIFFRACTIONr_scbond_it3.9265903
X-RAY DIFFRACTIONr_scangle_it5.3567795
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 75 -
Rwork0.254 1344 -
obs--86.26 %
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)
115.04983.42363.1153.28312.15115.4297-0.1693-0.2780.65420.068-0.0204-0.1246-0.3716-0.23710.18970.08440.01750.00280.07410.00720.105213.994730.369211.006
28.2407-1.6235-3.06961.61440.68823.1132-0.10930.14410.37540.08330.002-0.1082-0.0973-0.070.10730.1043-0.0205-0.00160.09780.01470.115916.477129.820914.0176
312.4349-8.19856.47111.5261-9.236413.2887-0.05770.21560.25450.2984-0.08220.2917-0.0399-0.5870.13990.13740.0125-0.00170.0718-0.04950.0244-2.018728.828322.0459
416.5423-13.082-1.014118.41052.76956.03980.0292-0.2915-0.14980.13690.2521-0.17730.60050.2774-0.28130.1601-0.02870.03850.0601-0.04380.05288.430619.837326.507
51.28574.6852.193630.4436.72253.86350.168-0.017-0.38740.79320.3971-1.77540.1030.1207-0.56510.06830.0204-0.0470.0915-0.08360.209216.89214.253619.3507
64.6425-4.3305-2.172312.47482.59261.0545-0.1134-0.26910.3790.33630.2048-0.198-0.0188-0.0536-0.09140.07240.0183-0.01750.1162-0.01830.032611.840132.332121.7929
72.42393.45693.06914.94074.53556.2417-0.0670.0261-0.0927-0.19060.1819-0.1998-0.1656-0.1299-0.11490.04210.0170.01340.07880.00290.124113.009514.51815.2969
82.51830.31321.35561.95380.67516.2614-0.03080.3291-0.0625-0.15920.1166-0.4217-0.04310.343-0.08580.03480.00230.01430.0801-0.03660.132213.72841.23513.1702
94.2231-0.4836-2.36775.59945.397210.8585-0.0599-0.16630.34330.91690.1038-0.39630.3521-0.1763-0.04390.19470.0326-0.0890.0216-0.01510.10238.47656.030321.587
103.1852-0.5011-6.19540.7691-1.408425.09980.28860.12720.64940.28550.08960.278-0.7982-0.2032-0.37820.08790.00720.04620.0241-0.01470.15681.36212.658416.992
1112.7803-5.8355-2.678810.5104-0.58370.9776-0.1051-0.18450.4249-0.06240.165-0.84060.02680.0416-0.05990.01810.0030.00450.1121-0.03450.162716.145911.18878.0486
121.1041-3.38412.082510.3727-6.3853.9616-0.21440.05590.02340.2978-0.0811-0.1489-0.1756-0.09190.29550.03160.02790.00450.07720.02820.19399.862917.572911.3878
1314.73242.6855-7.242814.975-6.122612.4163-0.14191.1454-1.0904-1.5268-0.2378-0.26540.6168-0.35410.37970.15890.03980.03030.0539-0.04970.03274.824122.3402-0.368
146.4372.26680.69090.80660.37342.113-0.081-0.05120.24960.09320.04680.2027-0.0796-0.34540.03410.11880.01340.03340.1054-0.0050.0799-9.44645.822116.1225
153.1417-0.5189-3.99132.16181.80798.99420.03550.2291-0.0232-0.02830.01450.0343-0.0153-0.1749-0.050.06180.0028-0.00980.0912-0.00080.07372.56311.92186.504
1619.92981.70486.56990.60071.48314.031-0.5520.58951.809-0.6041-0.118-0.1642-0.7686-0.17230.670.10630.0585-0.010.06920.04160.1436-7.78325.6136-1.8099
175.4594-2.3681-1.09054.29921.24833.00140.0290.1979-0.0624-0.0517-0.13710.02030.083-0.260.10820.1080.0043-0.00030.1703-0.04120.0718-5.1793-2.47680.3228
188.8504-2.123-3.49832.9972.23056.4285-0.05410.3135-0.34860.1908-0.06420.09170.5-0.36850.11830.1543-0.0533-0.00660.0811-0.00310.088-2.0269-6.89110.9714
195.3547-2.47670.03455.33921.90625.6202-0.0479-0.3325-0.240.60230.1574-0.37760.7110.2536-0.10950.20070.0054-0.05110.01920.01790.08896.7116-7.428117.7445
206.03312.94752.71965.07772.57996.62460.1081-0.0413-0.19380.73040.0997-0.63850.52550.2296-0.20780.13020.0786-0.10050.0301-0.02970.127515.7144-4.353615.5225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 327 - 29
2X-RAY DIFFRACTION2AA33 - 5130 - 48
3X-RAY DIFFRACTION3AA52 - 6149 - 58
4X-RAY DIFFRACTION4AA62 - 7159 - 68
5X-RAY DIFFRACTION5AA72 - 8069 - 77
6X-RAY DIFFRACTION6AA81 - 9278 - 89
7X-RAY DIFFRACTION7AA93 - 10590 - 102
8X-RAY DIFFRACTION8AA106 - 122103 - 119
9X-RAY DIFFRACTION9AA123 - 134120 - 131
10X-RAY DIFFRACTION10AA135 - 143132 - 140
11X-RAY DIFFRACTION11AA144 - 153141 - 150
12X-RAY DIFFRACTION12AA154 - 160151 - 157
13X-RAY DIFFRACTION13AA161 - 166158 - 163
14X-RAY DIFFRACTION14AA180 - 194177 - 191
15X-RAY DIFFRACTION15AA195 - 211192 - 208
16X-RAY DIFFRACTION16AA212 - 219209 - 216
17X-RAY DIFFRACTION17AA220 - 238217 - 235
18X-RAY DIFFRACTION18AA239 - 256236 - 253
19X-RAY DIFFRACTION19AA257 - 266254 - 263
20X-RAY DIFFRACTION20AA267 - 278264 - 275

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