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- PDB-2v8q: Crystal structure of the regulatory fragment of mammalian AMPK in... -

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Basic information

Entry
Database: PDB / ID: 2v8q
TitleCrystal structure of the regulatory fragment of mammalian AMPK in complexes with AMP
Components
  • 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
  • 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2
  • 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
KeywordsTRANSFERASE / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / MAGNESIUM / CBS DOMAIN
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 / negative regulation of tubulin deacetylation / histone H2BS36 kinase activity / cold acclimation / AMP-activated protein kinase activity / lipid droplet disassembly / Lipophagy / phosphatidylethanolamine biosynthetic process / regulation of carbon utilization / positive regulation of skeletal muscle tissue development / CAMKK-AMPK signaling cascade / import into nucleus / phosphatidylcholine biosynthetic process / regulation of vesicle-mediated transport / protein localization to lysosome / negative regulation of hepatocyte apoptotic process / positive regulation of fatty acid oxidation / negative regulation of T cell mediated immune response to tumor cell / Carnitine shuttle / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / nucleotide-activated protein kinase complex / protein kinase regulator activity / regulation of vascular permeability / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / protein K6-linked ubiquitination / regulation of glycolytic process / : / protein localization to lipid droplet / negative regulation of protein localization to nucleus / response to caffeine / tau-protein kinase activity / lysosome organization / cholesterol biosynthetic process / negative regulation of T cell activation / Macroautophagy / lipid biosynthetic process / cellular response to stress / AMP binding / hepatocyte apoptotic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / fatty acid oxidation / positive regulation of release of cytochrome c from mitochondria / motor behavior / TORC1 signaling / positive regulation of translational initiation / cellular response to ethanol / fatty acid homeostasis / negative regulation of lipid catabolic process / response to UV / autophagosome assembly / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / energy homeostasis / negative regulation of TORC1 signaling / negative regulation of insulin receptor signaling pathway / positive regulation of adipose tissue development / positive regulation of TORC1 signaling / negative regulation of translational initiation / positive regulation of autophagy / cellular response to calcium ion / cellular response to nutrient levels / positive regulation of gluconeogenesis / positive regulation of glycolytic process / cellular response to amino acid starvation / cellular response to starvation / regulation of microtubule cytoskeleton organization / response to activity / positive regulation of D-glucose import across plasma membrane / response to gamma radiation / protein localization to plasma membrane / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / circadian regulation of gene expression / response to hydrogen peroxide / cellular response to glucose stimulus / neuron cellular homeostasis / ADP binding / regulation of circadian rhythm / response to estrogen / protein destabilization / cellular response to xenobiotic stimulus / autophagy / glucose metabolic process / positive regulation of T cell activation / Wnt signaling pathway / cellular response to hydrogen peroxide / fatty acid biosynthetic process
Similarity search - Function
Double Stranded RNA Binding Domain - #60 / Double Stranded RNA Binding 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 ...Double Stranded RNA Binding Domain - #60 / Double Stranded RNA Binding 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 / Other non-globular / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Special / 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 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: 2.1 Å
AuthorsXiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. ...Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
CitationJournal: Nature / Year: 2007
Title: Structural Basis for AMP Binding to Mammalian AMP-Activated Protein Kinase
Authors: Xiao, B. / Heath, R. / Saiu, P. / Leiper, F.C. / Leone, P. / Jing, C. / Walker, P.A. / Haire, L. / Eccleston, J.F. / Davis, C.T. / Martin, S.R. / Carling, D. / Gamblin, S.J.
History
DepositionAug 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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-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)66,1526
Polymers65,1113
Non-polymers1,0423
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-49 kcal/mol
Surface area30320 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.522, 119.390, 129.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17635.799 Da / Num. of mol.: 1 / Fragment: RESIDUES 396-548
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
#2: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 / AMP-ACTIVATED PROTEIN KINASE / AMPK BETA-2 CHAIN


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 / AMP-ACTIVATED PROTEIN KINASE / AMPK GAMMA-1 CHAIN / 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
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG ...THE FIRST FOUR RESIDUES (GSMA) OF THE SEQUENCE OF CHAIN A ARE GENERATED FROM THE POST HIS-TAG CLEAVAGE THE FIRST RESIDUES (M) OF THE SEQUENCE OF CHAIN B IS GENERATED BY THE WAY IT WAS CLONED INTO THE VECTOR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 42012 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.644 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2234 5 %RANDOM
Rwork0.212 ---
obs0.213 42012 99 %-
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: 44.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--3.06 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 69 428 4381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224044
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9855491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4755474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23323.314172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37915718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9411525
X-RAY DIFFRACTIONr_chiral_restr0.110.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022935
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21867
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2364
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6821.52452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15723919
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43531803
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2334.51572
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: 2.1→2.21 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.298 308
Rwork0.263 5903
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)
11.5999-0.68120.78863.3406-1.47495.218-0.06770.07310.0023-0.1302-0.1409-0.0138-0.1520.45080.20860.0278-0.0765-0.017-0.17730.028-0.096219.70173.30511.257
21.4078-1.53721.04233.0635-3.61735.2095-0.1041-0.26740.05940.27660.032-0.0624-0.6652-0.31980.07210.18170.002-0.0246-0.1799-0.0207-0.041813.74377.13218.173
33.8083-0.57182.24130.4347-0.24421.34360.03450.2486-0.0285-0.0464-0.1273-0.15260.0530.34670.09280.03580.00860.0515-0.00190.1520.016635.68257.68631.437
41.09230.3548-0.42031.7073-1.42892.7792-0.0389-0.0185-0.0918-0.22440.18910.15680.3833-0.1929-0.15020.0654-0.0436-0.0308-0.1480.07270.004511.2247.90335.042
52.6590.48060.45752.57870.16862.18850.0639-0.2307-0.07840.0459-0.00490.10870.1142-0.0525-0.0590.03470.03290.0232-0.15170.078-0.037616.60842.74154.413
63.64310.35340.59071.8763-0.22044.54180.1641-0.16410.51410.1617-0.104-0.0889-0.44990.2731-0.06020.0464-0.03210.0514-0.12250.01390.060232.38457.02951.822
70.0981-0.20260.25980.4695-0.40261.0409-0.04410.0103-0.0022-0.07090.02960.00080.0717-0.00230.01440.0312-0.01350.0119-0.12490.0499-0.002420.70758.35232.538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A393 - 469
2X-RAY DIFFRACTION1A524 - 548
3X-RAY DIFFRACTION2B190 - 222
4X-RAY DIFFRACTION2B233 - 272
5X-RAY DIFFRACTION3E48 - 128
6X-RAY DIFFRACTION4E23 - 47
7X-RAY DIFFRACTION4E129 - 183
8X-RAY DIFFRACTION5E184 - 203
9X-RAY DIFFRACTION5E275 - 326
10X-RAY DIFFRACTION6E204 - 274
11X-RAY DIFFRACTION6E1327 - 1329
12X-RAY DIFFRACTION7A - E2001 - 2291

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