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- PDB-2yza: Crystal structure of kinase domain of Human 5'-AMP-activated prot... -

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Basic information

Entry
Database: PDB / ID: 2yza
TitleCrystal structure of kinase domain of Human 5'-AMP-activated protein kinase alpha-2 subunit mutant (T172D)
Components5'-AMP-activated protein kinase catalytic subunit alpha-2
KeywordsTRANSFERASE / Signaling protein / Serine/threonine protein kinase / Phosphorylation / ATP-binding / Nucleotide-binding / Cholesterol biosynthesis / Fatty acid biosynthesis / Lipid synthesis / glucose metabolism / Magnesium / Metal-binding / Serine/threonine-protein kinase / Steroid biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of peptidyl-lysine acetylation / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / lipid droplet disassembly / Lipophagy / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle ...positive regulation of peptidyl-lysine acetylation / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase / [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase activity / regulation of stress granule assembly / AMPK inhibits chREBP transcriptional activation activity / lipid droplet disassembly / Lipophagy / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / Carnitine shuttle / negative regulation of hepatocyte apoptotic process / negative regulation of TOR signaling / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / Nuclear events mediated by NFE2L2 / protein localization to lipid droplet / lipid biosynthetic process / negative regulation of tubulin deacetylation / Macroautophagy / response to muscle activity / cholesterol biosynthetic process / positive regulation of macroautophagy / regulation of macroautophagy / fatty acid homeostasis / cellular response to nutrient levels / cellular response to glucose starvation / Activation of AMPK downstream of NMDARs / energy homeostasis / positive regulation of protein localization / negative regulation of TORC1 signaling / positive regulation of autophagy / protein serine/threonine/tyrosine kinase activity / regulation of microtubule cytoskeleton organization / cellular response to calcium ion / positive regulation of glycolytic process / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / cellular response to glucose stimulus / regulation of circadian rhythm / autophagy / Wnt signaling pathway / cytoplasmic stress granule / fatty acid biosynthetic process / rhythmic process / cellular response to prostaglandin E stimulus / glucose homeostasis / cellular response to xenobiotic stimulus / cellular response to oxidative stress / 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 / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / nuclear speck / ciliary basal body / protein phosphorylation / axon / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / neuronal cell body / dendrite / chromatin binding / negative regulation of apoptotic process / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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. / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsSaijo, S. / Takagi, T. / Yoshikawa, S. / Kishishita, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural basis for compound C inhibition of the human AMP-activated protein kinase alpha 2 subunit kinase domain
Authors: Handa, N. / Takagi, T. / Saijo, S. / Kishishita, S. / Takaya, D. / Toyama, M. / Terada, T. / Shirouzu, M. / Suzuki, A. / Lee, S. / Yamauchi, T. / Okada-Iwabu, M. / Iwabu, M. / Kadowaki, T. / ...Authors: Handa, N. / Takagi, T. / Saijo, S. / Kishishita, S. / Takaya, D. / Toyama, M. / Terada, T. / Shirouzu, M. / Suzuki, A. / Lee, S. / Yamauchi, T. / Okada-Iwabu, M. / Iwabu, M. / Kadowaki, T. / Minokoshi, Y. / Yokoyama, S.
History
DepositionMay 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Oct 25, 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)31,5721
Polymers31,5721
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.187, 67.336, 50.651
Angle α, β, γ (deg.)90.00, 91.26, 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 / 5'-AMP-activated protein kinase alpha-2 subunit / AMPK alpha-2 chain


Mass: 31571.730 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: T172D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAA2, AMPK, AMPK2 / Plasmid: PX060824-01 / Production host: Cell-free protein synthesis
References: UniProt: P54646, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 0.1M Tris-HCl pH8.9, 16% PEG4000, 15% isopropanol, 0.1M Ammonium sulfate, Protein solution: 5mM AMPPNP, 5mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2006 / Details: rhodium coated mirror
RadiationMonochromator: fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 4913 / % possible obs: 94.3 % / Redundancy: 3 % / Biso Wilson estimate: 48.3 Å2 / Rsym value: 0.106 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 126 / Rsym value: 0.251 / % possible all: 51.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H6D

2h6d


Resolution: 3.02→25 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.769 / SU B: 25.942 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.673 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.308 484 9.9 %RANDOM
Rwork0.227 ---
obs0.235 4422 93.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.51 Å2
2--0.15 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 3.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 0 10 2073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8731.9622854
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4055256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40222.82692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5111514
X-RAY DIFFRACTIONr_chiral_restr0.0550.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021568
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.2861
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21417
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1771.51321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31522070
X-RAY DIFFRACTIONr_scbond_it0.263891
X-RAY DIFFRACTIONr_scangle_it0.4444.5784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.02→3.094 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 17 -
Rwork0.241 171 -
obs-188 49.47 %

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