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- PDB-2ya3: STRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 2ya3
TitleSTRUCTURE OF THE REGULATORY FRAGMENT OF MAMMALIAN AMPK IN COMPLEX WITH COUMARIN ADP
Components
  • (5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT ...) x 2
  • 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION
Function / homology
Function and homology information


eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / histone H2BS36 kinase activity ...eukaryotic elongation factor-2 kinase activator activity / Energy dependent regulation of mTOR by LKB1-AMPK / positive regulation of mitochondrial transcription / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / [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 / regulation of peptidyl-serine phosphorylation / cold acclimation / positive regulation of peptidyl-lysine acetylation / lipid droplet disassembly / Lipophagy / regulation of bile acid secretion / positive regulation of fatty acid oxidation / positive regulation of skeletal muscle tissue development / import into nucleus / CAMKK-AMPK signaling cascade / regulation of vesicle-mediated transport / nucleotide-activated protein kinase complex / : / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / tau-protein kinase / negative regulation of hepatocyte apoptotic process / protein kinase regulator activity / cellular response to ethanol / negative regulation of TOR signaling / protein localization to lipid droplet / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / response to caffeine / motor behavior / bile acid and bile salt transport / positive regulation of protein targeting to mitochondrion / lipid biosynthetic process / AMP-activated protein kinase activity / negative regulation of tubulin deacetylation / tau-protein kinase activity / Macroautophagy / cholesterol biosynthetic process / AMP binding / fatty acid oxidation / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / response to UV / positive regulation of protein localization / energy homeostasis / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of glycolytic process / cellular response to calcium ion / response to gamma radiation / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of D-glucose import / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / ADP binding / regulation of circadian rhythm / response to hydrogen peroxide / Wnt signaling pathway / autophagy / fatty acid biosynthetic process / cellular response to hydrogen peroxide / response to estrogen / neuron cellular homeostasis / glucose metabolic process / cellular response to prostaglandin E stimulus / rhythmic process / cellular response to xenobiotic stimulus / positive regulation of cold-induced thermogenesis / glucose homeostasis / cellular response to oxidative stress / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / negative regulation of translation / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / response to xenobiotic stimulus / protein phosphorylation / apical plasma membrane / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / chromatin binding / dendrite / positive regulation of cell population proliferation
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 MONOPHOSPHATE / Chem-J7V / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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)68,6486
Polymers66,9623
Non-polymers1,6863
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-39 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.943, 124.060, 125.315
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 407-555
Source method: isolated from a genetically manipulated source
Details: THE RESIDUES FROM A 393-395 AND 545-550 ARE ARTIFICIAL AS A RESULT OF CLONING STRATEGY
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 SUBUNIT ALPHA-1 / AMPK GAMMA1 / AMPK SUBUNIT GAMMA-1 / AMPKG


Mass: 37434.094 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-330
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, 145 molecules

#4: Chemical ChemComp-J7V / 3'-(7-diethylaminocoumarin-3-carbonylamino)-3'-deoxy-ADP


Mass: 669.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N7O12P2
#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.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN SEQUENCE HAS HIS-TAG MSHHHHHHSGLVPRG AT THE N- TERMINAL, AND SMA 393-395 AND NSCTVN 545- ...THE PROTEIN SEQUENCE HAS HIS-TAG MSHHHHHHSGLVPRG AT THE N- TERMINAL, AND SMA 393-395 AND NSCTVN 545-550 ARE CLONING ARTIFACTS. 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→28.2 Å / Num. obs: 25251 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V8Q

2v8q


Resolution: 2.51→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.976 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26271 1345 5.1 %RANDOM
Rwork0.22264 ---
obs0.22463 25251 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.337 Å2
Baniso -1Baniso -2Baniso -3
1--2.85 Å20 Å20 Å2
2--2.66 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.51→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 113 142 4060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9995455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69823.212165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89215704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4761524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212910
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_it0.4341.52354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80623850
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.83331657
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4894.51605
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: 2.512→2.577 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 99 -
Rwork0.304 1826 -
obs--98.31 %
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)
10.80930.9843-0.52182.3232-2.73144.3925-0.006-0.01550.0274-0.0458-0.1263-0.06110.1580.11490.13230.05950.01760.02620.08010.0260.0577-7.13-16.02749.851
24.53670.6923-1.8860.1814-0.3180.79750.1098-0.24290.09390.0698-0.1015-0.0653-0.06590.1415-0.00830.0427-0.0237-0.04450.2520.11040.136811.3042.0132.881
31.7699-0.31190.29642.6707-1.3432.49660.0052-0.03590.10.19940.12640.1826-0.319-0.1331-0.13150.04410.02960.02650.09760.05170.0907-13.02611.9230.218
44.201-0.2263-0.81882.3088-0.89422.638-0.00910.11930.1492-0.07480.02090.1215-0.12040.0606-0.01180.029-0.0314-0.03580.07240.05020.0595-7.66218.16910.565
50.36580.2669-0.38290.7686-0.72841.3233-0.04360.0604-0.076-0.1094-0.1062-0.08440.0750.15930.14980.0225-0.0035-0.01370.16550.04230.13656.213.516.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 469
2X-RAY DIFFRACTION1A524 - 549
3X-RAY DIFFRACTION1B190 - 219
4X-RAY DIFFRACTION1B235 - 272
5X-RAY DIFFRACTION2E48 - 128
6X-RAY DIFFRACTION3E25 - 47
7X-RAY DIFFRACTION3E129 - 183
8X-RAY DIFFRACTION4E184 - 203
9X-RAY DIFFRACTION4E275 - 324
10X-RAY DIFFRACTION5E204 - 274
11X-RAY DIFFRACTION5E1325 - 1327
12X-RAY DIFFRACTION5A2001 - 2032
13X-RAY DIFFRACTION5B2001 - 2020
14X-RAY DIFFRACTION5E2001 - 2090

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