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- PDB-5ezv: X-ray crystal structure of AMP-activated protein kinase alpha-2/a... -

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Basic information

Entry
Database: PDB / ID: 5ezv
TitleX-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid)
Components
  • (5'-AMP-activated protein kinase subunit ...) x 2
  • 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
KeywordsTRANSFERASE / serine/threonine kinase / allosteric activation / nucleotide-binding
Function / homology
Function and homology information


negative regulation of glucosylceramide biosynthetic process / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / cAMP-dependent protein kinase regulator activity ...negative regulation of glucosylceramide biosynthetic process / nail development / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / positive regulation of mitochondrial transcription / AMPK inhibits chREBP transcriptional activation activity / histone H2BS36 kinase activity / cold acclimation / cAMP-dependent protein kinase regulator activity / AMP-activated protein kinase activity / 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 / negative regulation of hepatocyte apoptotic process / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / positive regulation of T cell mediated immune response to tumor cell / tau-protein kinase / protein kinase regulator activity / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / response to caffeine / positive regulation of protein targeting to mitochondrion / regulation of glycolytic process / cAMP-dependent protein kinase activity / protein localization to lipid droplet / tau-protein kinase activity / negative regulation of tubulin deacetylation / AMP binding / cellular response to stress / Macroautophagy / cholesterol biosynthetic process / lipid biosynthetic process / response to muscle activity / fatty acid oxidation / motor behavior / positive regulation of protein kinase activity / cellular response to ethanol / positive regulation of macroautophagy / regulation of macroautophagy / fatty acid homeostasis / negative regulation of lipid catabolic process / cellular response to nutrient levels / response to UV / cellular response to glucose starvation / energy homeostasis / Activation of AMPK downstream of NMDARs / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of adipose tissue development / positive regulation of gluconeogenesis / protein serine/threonine/tyrosine kinase activity / positive regulation of autophagy / negative regulation of insulin receptor signaling pathway / cellular response to calcium ion / regulation of microtubule cytoskeleton organization / positive regulation of glycolytic process / response to activity / response to gamma radiation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cellular response to glucose stimulus / positive regulation of cholesterol biosynthetic process / regulation of circadian rhythm / neuron cellular homeostasis / ADP binding / positive regulation of T cell activation / autophagy / response to estrogen / tau protein binding / cellular response to xenobiotic stimulus / Wnt signaling pathway / cellular response to hydrogen peroxide / glucose metabolic process / cytoplasmic stress granule / fatty acid biosynthetic process / rhythmic process / glucose homeostasis / cellular response to prostaglandin E stimulus / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / spermatogenesis / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / regulation of cell cycle / nuclear speck / cilium / ciliary basal body / apical plasma membrane
Similarity search - Function
PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / 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 / : ...PRKAA2, UBA-like autoinhibitory domain / 5'-AMP-activated protein kinase catalytic subunit alpha-2, C-terminal / 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 / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Immunoglobulin E-set / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C1V / Chem-C2Z / STAUROSPORINE / 5'-AMP-activated protein kinase subunit gamma-1 / 5'-AMP-activated protein kinase catalytic subunit alpha-2 / 5'-AMP-activated protein kinase catalytic subunit alpha-1 / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLangendorf, C.G. / Kemp, B.E.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding.
Authors: Langendorf, C.G. / Ngoei, K.R. / Scott, J.W. / Ling, N.X. / Issa, S.M. / Gorman, M.A. / Parker, M.W. / Sakamoto, K. / Oakhill, J.S. / Kemp, B.E.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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/alpha-1 RIM SWAP chimera
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
D: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,84414
Polymers265,2666
Non-polymers2,5788
Water1,51384
1
A: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
B: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9227
Polymers132,6333
Non-polymers1,2894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-85 kcal/mol
Surface area41600 Å2
MethodPISA
2
C: 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
D: 5'-AMP-activated protein kinase subunit beta-1
F: 5'-AMP-activated protein kinase subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,9227
Polymers132,6333
Non-polymers1,2894
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14060 Å2
ΔGint-88 kcal/mol
Surface area41800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.608, 134.112, 141.287
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein 5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera / AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA ...AMPK subunit alpha-2 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / AMPK subunit alpha-1 / Acetyl-CoA carboxylase kinase / ACACA kinase / Hydroxymethylglutaryl-CoA reductase kinase / HMGCR kinase / Tau-protein kinase PRKAA1


Mass: 63902.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2, PRKAA1, AMPK1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P54646, UniProt: Q13131, non-specific serine/threonine protein kinase, EC: 2.7.11.27, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase

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5'-AMP-activated protein kinase subunit ... , 2 types, 4 molecules BDEF

#2: Protein 5'-AMP-activated protein kinase subunit beta-1 / AMPKb


Mass: 30504.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAB1, AMPK / Plasmid: pCOLA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9Y478
#3: Protein 5'-AMP-activated protein kinase subunit gamma-1 / AMPKg


Mass: 38225.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAG1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P54619

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Non-polymers , 4 types, 92 molecules

#4: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#5: Chemical ChemComp-C1V / 3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile


Mass: 360.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12N2O3S
#6: Chemical
ChemComp-C2Z / 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid / [5-(5-hydroxy-1,2-oxazol-3-yl)furan-2-yl]phosphonic acid


Mass: 231.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6NO6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 8 % PEG 3350, 0.1 M MgCl2, 1.0 % glucose, 0.001 % cocamidopropyl betaine, 0.1 M imidazole
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.99→49.3 Å / Num. all: 182062 / Num. obs: 56584 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 87.43 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.053 / Net I/σ(I): 10.1 / Num. measured all: 182062 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.99-3.083.20.4682.61456345540.7680.31298
12.69-49.33.10.04920.523567640.9890.03498.2

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER-TNT1.10.0refinement
PDB_EXTRACT3.15data extraction
PHASER6.3.0phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHX

4zhx


Resolution: 2.99→49.3 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8933 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 4.496 / SU Rfree Blow DPI: 0.359
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2867 5.07 %RANDOM
Rwork0.2243 ---
obs0.2254 56562 99.3 %-
Displacement parametersBiso max: 175.46 Å2 / Biso mean: 68.78 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.016 Å20 Å2-3.0348 Å2
2---8.7512 Å20 Å2
3---6.7352 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 2.99→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14408 0 182 84 14674
Biso mean--59.39 46.94 -
Num. residues----1856
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4985SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2179HARMONIC5
X-RAY DIFFRACTIONt_it14989HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1979SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16268SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14989HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg20434HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion1.54
X-RAY DIFFRACTIONt_other_torsion17.91
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2795 196 4.77 %
Rwork0.2731 3913 -
all0.2734 4109 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 119.3968 Å / Origin y: -35.0872 Å / Origin z: 35.6237 Å
111213212223313233
T0.406 Å2-0.0745 Å20.0325 Å2-0.3918 Å2-0.0152 Å2--0.392 Å2
L0.1111 °2-0.1907 °20.1086 °2-0.297 °2-0.1722 °2--0.0977 °2
S0.0061 Å °0.0191 Å °0.033 Å °0.0155 Å °0.0096 Å °0.025 Å °0.0165 Å °-0.054 Å °-0.0157 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A8 - 545
2X-RAY DIFFRACTION1{ *|* }A8 - 545
3X-RAY DIFFRACTION1{ *|* }B78 - 270
4X-RAY DIFFRACTION1{ *|* }B78 - 270
5X-RAY DIFFRACTION1{ *|* }C9 - 545
6X-RAY DIFFRACTION1{ *|* }C9 - 545
7X-RAY DIFFRACTION1{ *|* }D77 - 269
8X-RAY DIFFRACTION1{ *|* }E24 - 326
9X-RAY DIFFRACTION1{ *|* }F25 - 324
10X-RAY DIFFRACTION1{ *|* }G5 - 8
11X-RAY DIFFRACTION1{ *|* }H1 - 85

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