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- PDB-2y8q: Structure of the regulatory fragment of mammalian AMPK in complex... -

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Basic information

Entry
Database: PDB / ID: 2y8q
TitleStructure of the regulatory fragment of mammalian AMPK in complex with one ADP
Components
  • (5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ...) x 2
  • 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
KeywordsTRANSFERASE / ADP / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / positive regulation of mitochondrial transcription / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / cold acclimation / lipid droplet disassembly / Lipophagy / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / positive regulation of fatty acid oxidation / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / cellular response to ethanol / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / protein localization to lipid droplet / motor behavior / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / cellular response to stress / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / fatty acid homeostasis / cellular response to nutrient levels / negative regulation of lipid catabolic process / response to UV / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / energy homeostasis / positive regulation of protein localization / positive regulation of adipose tissue development / negative regulation of TORC1 signaling / positive regulation of autophagy / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to calcium ion / positive regulation of glycolytic process / response to activity / response to gamma radiation / positive regulation of D-glucose import / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / regulation of circadian rhythm / ADP binding / response to hydrogen peroxide / autophagy / positive regulation of T cell activation / cellular response to hydrogen peroxide / Wnt signaling pathway / neuron cellular homeostasis / response to estrogen / glucose metabolic process / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity
Similarity search - Function
Kinase associated domain 1, KA1 / PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain ...Kinase associated domain 1, KA1 / PRKAA1, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase alpha 1 catalytic subunit, C-terminal / : / AMP-activated protein kinase, alpha subunit, autoinhibitory domain / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / 5'-AMP-activated protein kinase subunit beta-2 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit gamma-1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. ...Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J.
CitationJournal: Nature / Year: 2011
Title: Structure of Mammalian Ampk and its Regulation by Adp
Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. ...Authors: Xiao, B. / Sanders, M.J. / Underwood, E. / Heath, R. / Mayer, F. / Carmena, D. / Jing, C. / Walker, P.A. / Eccleston, J.F. / Haire, L.F. / Saiu, P. / Howell, S.A. / Aasland, R. / Martin, S.R. / Carling, D. / Gamblin, S.J.
History
DepositionFeb 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
B: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2
E: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7365
Polymers66,9623
Non-polymers7742
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-45.3 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.026, 119.918, 130.150
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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Protein , 1 types, 1 molecules A

#1: Protein 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 / AMPK SUBUNIT ALPHA-1


Mass: 19486.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 406-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P54645, non-specific serine/threonine protein kinase

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5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ... , 2 types, 2 molecules BE

#2: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 / AMPK SUBUNIT BETA-2


Mass: 10040.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 187-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O43741
#3: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMPK GAMMA1 / AMPK SUBUNIT GAMMA-1 / AMPKG


Mass: 37434.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80385

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Non-polymers , 3 types, 58 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsADENOSINE MONOPHOSPHATE (AMP): BINDING SITE 4 ADENOSINE-5'-DIPHOSPHATE (ADP): BINDING SITE 1
Sequence detailsTHE DNA SEQUENCE WITH HIS-TAG, MSHHHHHHSGLVPRG AND THE ARTIFACTS, SMA (393-395) AND NSCTVN (545-550) ...THE DNA SEQUENCE WITH HIS-TAG, MSHHHHHHSGLVPRG AND THE ARTIFACTS, SMA (393-395) AND NSCTVN (545-550) AS A RESULT OF CLONING STRATEGY. B 186 METHIONINE IS AN ARTIFACT, CREATED BY CLONING.

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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: 2.86 Å3/Da / Density % sol: 62 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 12, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 17426 / % possible obs: 93.8 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8Q

2v8q


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.905 / SU B: 32.605 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.108 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 952 5.2 %RANDOM
Rwork0.232 ---
obs0.234 17426 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.458 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2--3.52 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 50 56 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9785456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0245474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35823.314172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27515716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1381525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212924
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5271.52398
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.98623921
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.03831622
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8324.51535
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 57 -
Rwork0.394 1261 -
obs--92.62 %
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)
11.85111.5587-0.36733.4229-4.20447.8242-0.14540.054-0.0025-0.4112-0.1909-0.23230.77090.29330.33630.26450.08550.05560.13330.02880.152717.32344.53351.199
210.70052.4117-4.74230.5539-1.05142.13810.016-0.8534-0.24870.0339-0.1473-0.06730.02250.50570.13130.22160.0467-0.05750.59280.27140.383435.80162.02533.546
32.044-0.36460.48222.9646-1.67096.7351-0.08660.23640.15890.39850.12070.2224-0.7524-0.2395-0.03410.12450.04120.03270.09240.06740.206411.19471.9730.068
45.0311-0.3783-0.894.4093-1.04115.8891-0.10960.18070.1355-0.00190.06010.0429-0.28860.14180.04960.1148-0.0479-0.04740.05050.06060.104816.44677.23210.402
51.00510.4031-0.6861.5606-0.95973.0291-0.0829-0.1609-0.4669-0.1916-0.2801-0.26650.23430.63150.3630.15960.04710.02980.36110.09080.396132.2762.93414.424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A393 - 469
2X-RAY DIFFRACTION1A524 - 550
3X-RAY DIFFRACTION1B190 - 221
4X-RAY DIFFRACTION1B233 - 272
5X-RAY DIFFRACTION2E48 - 128
6X-RAY DIFFRACTION3E23 - 47
7X-RAY DIFFRACTION3E129 - 183
8X-RAY DIFFRACTION4E184 - 203
9X-RAY DIFFRACTION4E275 - 326
10X-RAY DIFFRACTION5E204 - 274
11X-RAY DIFFRACTION5E1327 - 1328
12X-RAY DIFFRACTION5A2001 - 2006
13X-RAY DIFFRACTION5B2001 - 2011
14X-RAY DIFFRACTION5E2001 - 2039

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