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- PDB-2oox: Crystal structure of the adenylate sensor from AMP-activated prot... -

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Basic information

Entry
Database: PDB / ID: 2oox
TitleCrystal structure of the adenylate sensor from AMP-activated protein kinase complexed with AMP
Components
  • Hypothetical protein C1556.08c in chromosome I
  • SNF1-like protein kinase ssp2
  • SPCC1919.03c protein
KeywordsTRANSFERASE / AMPK / kinase / AMP
Function / homology
Function and homology information


positive regulation of flocculation / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway ...positive regulation of flocculation / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway / regulation of carbon utilization / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / protein kinase regulator activity / regulation of glycolytic process / AMP binding / protein kinase activator activity / cellular response to glucose starvation / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / ADP binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / 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 ...N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / 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 / CBS-domain / CBS-domain / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / N-terminal domain of TfIIb / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Single Sheet / 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 / Roll / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / SNF1-like protein kinase ssp2 / 5'-AMP-activated protein kinase subunit beta / 5'-AMP-activated protein kinase subunit gamma
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsTownley, R. / Shapiro, L.
CitationJournal: Science / Year: 2007
Title: Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.
Authors: Townley, R. / Shapiro, L.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DEFINITIVE BIOLOGICAL UNIT IS A HETEROTRIMER (THERE ARE TWO SUCH TRIMERS: A+B+G AND C+D+E IN THE ASYMMETRIC UNIT), AND THAT THE DIMER OF THESE HETEROTRIMERS (SEE REMARK 350) IS ALSO PHYSIOLOGICALLY RELEVANT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Hypothetical protein C1556.08c in chromosome I
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Hypothetical protein C1556.08c in chromosome I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9628
Polymers128,2686
Non-polymers6942
Water11,746652
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Hypothetical protein C1556.08c in chromosome I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4814
Polymers64,1343
Non-polymers3471
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-59 kcal/mol
Surface area24550 Å2
MethodPISA, PQS
3
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Hypothetical protein C1556.08c in chromosome I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4814
Polymers64,1343
Non-polymers3471
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-56 kcal/mol
Surface area24680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.456, 97.392, 168.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein SNF1-like protein kinase ssp2


Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 440-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: ssp2, SPCC74.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O74536, non-specific serine/threonine protein kinase
#2: Protein SPCC1919.03c protein


Mass: 10865.345 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 203-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: SPCC1919.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78789
#3: Protein Hypothetical protein C1556.08c in chromosome I


Mass: 37364.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: SPAC1556.08c, SPAC1F12.01c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10343
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 6.2-7.2% PEG6000, 10% Ethylene glycol, 0.1M HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898, 0.97919
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979191
ReflectionResolution: 2.6→50 Å / Num. all: 38169 / Num. obs: 38081 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.1
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.469 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.317 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27348 1903 5 %RANDOM
Rwork0.20627 ---
all0.22008 ---
obs0.20975 36178 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--2.22 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8624 0 46 652 9322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.97712049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08451095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38323.877374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.98151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3641553
X-RAY DIFFRACTIONr_chiral_restr0.1250.21394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026591
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2720.24954
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.26106
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3020.2850
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3290.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.55631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78228915
X-RAY DIFFRACTIONr_scbond_it2.14833643
X-RAY DIFFRACTIONr_scangle_it3.4864.53133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 126 -
Rwork0.257 2581 -
obs--98.58 %

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