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

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Basic information

Entry
Database: PDB / ID: 2qre
TitleCrystal structure of the adenylate sensor from AMP-activated protein kinase in complex with 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide (ZMP)
Components
  • Protein C1556.08c
  • SNF1-like protein kinase ssp2
  • SPCC1919.03c protein
KeywordsTRANSFERASE / AMPK / 5-aminoimidazole-4-carboxamide 1-beta-D-ribofuranotide / ZMP / AICAR phosphate / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / CBS domain
Function / homology
Function and homology information


positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body ...positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / 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 / CAMKK-AMPK signaling cascade / protein kinase regulator activity / nucleotide-activated protein kinase complex / protein kinase activator activity / AMP binding / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / ADP binding / carbohydrate metabolic process / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / 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 / cytosol / cytoplasm
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / N-terminal domain of TfIIb / 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
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / 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 / FOURIER SYNTHESIS / Resolution: 3.01 Å
AuthorsJin, X. / Townley, R. / Shapiro, L.
CitationJournal: Structure / Year: 2007
Title: Structural Insight into AMPK Regulation: ADP Comes into Play.
Authors: Jin, X. / Townley, R. / Shapiro, L.
History
DepositionJul 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)129,0868
Polymers128,4106
Non-polymers6762
Water34219
1
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5434
Polymers64,2053
Non-polymers3381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
MethodPISA
2
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5434
Polymers64,2053
Non-polymers3381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.470, 78.146, 108.512
Angle α, β, γ (deg.)90.00, 124.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a heterotrimer (There are two such trimers: A+B+G and C+D+E in the asymmetric unit). The dimer of these heterotrimers is also physiologically relevant.

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Components

#1: Protein SNF1-like protein kinase ssp2


Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal residues:440-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: ssp2 / Plasmid: PSMT3 / 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 residues:203-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: 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 Protein C1556.08c


Mass: 37436.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: 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-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR / AICA ribonucleotide


Mass: 338.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N4O8P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6-10% PEG 3350, 0.1M sodium citrate, pH 5.5, 2mM ZMP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 21790 / Num. obs: 20826 / % possible obs: 89.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 4.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2232 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 200y

200y


Resolution: 3.01→41.34 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.847 / SU B: 46.792 / SU ML: 0.405 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.61 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29736 1048 5 %RANDOM
Rwork0.2354 ---
all0.303 20590 --
obs0.23853 19774 89.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-1.53 Å2
2---0.62 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 3.01→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 44 19 8193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228364
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.97911347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46551020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57823.757354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.108151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9071552
X-RAY DIFFRACTIONr_chiral_restr0.0940.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026174
X-RAY DIFFRACTIONr_nbd_refined0.2290.24019
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.241
X-RAY DIFFRACTIONr_mcbond_it0.3661.55298
X-RAY DIFFRACTIONr_mcangle_it0.65728379
X-RAY DIFFRACTIONr_scbond_it0.88933454
X-RAY DIFFRACTIONr_scangle_it1.4664.52967
LS refinement shellResolution: 3.01→3.089 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 77 -
Rwork0.253 1490 -
obs--92.34 %
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)
13.96180.61661.89534.7496-0.32154.02870.03390.37840.4312-0.18110.0482-0.07-0.39570.0645-0.0821-0.27320.07490.0223-0.04730.1394-0.2168-10.72822.19789.7239
27.25420.54511.16216.3762-0.94694.09670.7962-0.01731.05430.009-0.35661.0975-0.64440.6147-0.4396-0.20120.17740.12480.0322-0.029-0.0255-12.933629.84115.8414
36.42453.64011.37799.1051-1.11512.4956-0.0281-0.58510.1202-0.06890.04280.2251-0.377-0.4974-0.0147-0.26890.07190.0556-0.08330.0232-0.3764-11.82769.260121.2715
44.6015-0.7106-0.70147.12682.49643.7710.04230.6899-0.3336-0.67620.1839-0.47240.03340.6818-0.2263-0.2659-0.00970.03990.1679-0.1508-0.242237.5207-5.418512.4346
57.21651.28191.00290.7827-1.51795.73580.41530.4666-0.7399-0.00090.3452-0.68541.17810.6171-0.7605-0.02260.2821-0.16580.3053-0.015-0.170838.2113-11.689119.1903
616.73683.29042.42849.94551.22423.3236-0.3183-0.0422-0.15120.17350.3206-0.09590.51050.7521-0.0022-0.2768-0.00810.1275-0.06320.0121-0.465737.14218.482324.1968
73.4034-0.1048-0.29660.8068-0.12480.4702-0.0720.2924-0.4045-0.07250.0051-0.17650.2105-0.08970.067-0.198-0.0834-0.0277-0.0348-0.0116-0.1404-4.8995-8.730719.1821
84.39120.4851.47860.87810.23533.1930.1996-0.1032-0.13590.24950.0391-0.070.2898-0.2791-0.2387-0.1506-0.03830.0413-0.24240.0312-0.0962-0.5055-19.195535.4444
93.6551-0.36270.59881.42530.4861.1137-0.10230.38930.2817-0.28170.01160.1114-0.26420.29370.0907-0.1478-0.1295-0.0535-0.0620.0875-0.194930.831626.017721.0695
104.8046-0.1996-1.30661.7136-0.36321.7542-0.10920.07030.2688-0.06110.1016-0.0895-0.29730.33810.0076-0.0512-0.0551-0.112-0.19330.0127-0.088524.994836.629136.7641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA451 - 57612 - 137
2X-RAY DIFFRACTION2BB207 - 2456 - 44
3X-RAY DIFFRACTION3BB250 - 29749 - 96
4X-RAY DIFFRACTION4CD450 - 57611 - 137
5X-RAY DIFFRACTION5DE207 - 2476 - 46
6X-RAY DIFFRACTION6DE248 - 29747 - 96
7X-RAY DIFFRACTION7GC2 - 1722 - 172
8X-RAY DIFFRACTION8GC173 - 316173 - 316
9X-RAY DIFFRACTION9EF2 - 1722 - 172
10X-RAY DIFFRACTION10EF173 - 316173 - 316

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