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- PDB-3gqy: Activator-Bound Structure of Human Pyruvate Kinase M2 -

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Basic information

Entry
Database: PDB / ID: 3gqy
TitleActivator-Bound Structure of Human Pyruvate Kinase M2
ComponentsPyruvate kinase isozymes M1/M2
KeywordsTRANSFERASE / activator / Acetylation / Allosteric enzyme / Alternative splicing / Glycolysis / Kinase / Magnesium / Metal-binding / Phosphoprotein / Polymorphism / Pyruvate / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / histone H3T11 kinase activity / programmed cell death / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / histone H3T11 kinase activity / programmed cell death / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / Regulation of pyruvate metabolism / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / protein tyrosine kinase activity / collagen-containing extracellular matrix / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / mRNA binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / extracellular exosome / extracellular region / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase, C-terminal domain / Pyruvate Kinase; Chain: A, domain 1 / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DZG / 1,6-di-O-phosphono-beta-D-fructofuranose / L(+)-TARTARIC ACID / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. ...Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Inglese, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Activator-Bound Structures of Human Pyruvate Kinase M2
Authors: Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Authors: Hong, B. / Dimov, S. / Tempel, W. / Auld, D. / Thomas, C. / Boxer, M. / Jianq, J.-K. / Skoumbourdis, A. / Min, S. / Southall, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Inglese, J. / Park, H.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase isozymes M1/M2
B: Pyruvate kinase isozymes M1/M2
C: Pyruvate kinase isozymes M1/M2
D: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,37025
Polymers240,2004
Non-polymers3,17021
Water12,250680
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-100 kcal/mol
Surface area68570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.149, 152.952, 93.159
Angle α, β, γ (deg.)90.000, 103.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Pyruvate kinase isozymes M1/M2 / Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / ...Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / CTHBP / THBP1


Mass: 60050.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, PK2, PK3, PKM / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P14618, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 697 molecules

#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#5: Chemical ChemComp-DZG / 1-(2,3-dihydro-1,4-benzodioxin-6-ylsulfonyl)-4-[(4-methoxyphenyl)sulfonyl]piperazine


Mass: 454.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N2O7S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ATP, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 182520 / % possible obs: 96.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Χ2: 1.683 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.923.80.969176731.20794.3
1.92-1.993.80.674178971.31494.8
1.99-2.083.80.472179491.39195.4
2.08-2.193.80.325179891.42296
2.19-2.333.80.229181981.68496.5
2.33-2.513.80.157182351.6197.1
2.51-2.763.80.107183951.75697.8
2.76-3.163.80.067185701.98398.4
3.16-3.983.80.041186622.3798.8
3.98-303.80.03189522.01899.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZJH

1zjh


Resolution: 1.85→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.202 / SU B: 3.366 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2125 1.17 %Thin shells (sftools)
Rwork0.213 ---
obs0.213 181606 96.741 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0.653 Å2
2---0.083 Å20 Å2
3---0.413 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15056 0 195 680 15931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0110.02215487
X-RAY DIFFRACTIONf_bond_other_d0.0010.0210217
X-RAY DIFFRACTIONf_angle_refined_deg1.0141.97821041
X-RAY DIFFRACTIONf_angle_other_deg0.804324954
X-RAY DIFFRACTIONf_dihedral_angle_1_deg4.99452029
X-RAY DIFFRACTIONf_dihedral_angle_2_deg32.91123.828593
X-RAY DIFFRACTIONf_dihedral_angle_3_deg11.544152495
X-RAY DIFFRACTIONf_dihedral_angle_4_deg13.5715107
X-RAY DIFFRACTIONf_chiral_restr0.0580.22465
X-RAY DIFFRACTIONf_gen_planes_refined0.0030.02117348
X-RAY DIFFRACTIONf_gen_planes_other0.0010.022957
X-RAY DIFFRACTIONf_mcbond_it0.977210129
X-RAY DIFFRACTIONf_mcbond_other0.2224130
X-RAY DIFFRACTIONf_mcangle_it1.583316191
X-RAY DIFFRACTIONf_scbond_it1.10125358
X-RAY DIFFRACTIONf_scangle_it1.73234849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8980.3561370.345128331379394.033
1.898-1.9490.2831220.302125141341194.221
1.949-2.0060.2741230.28122601305294.874
2.006-2.0670.2721220.254120281275495.264
2.067-2.1340.2851130.233116961233995.705
2.134-2.2090.2751260.232113081190996.011
2.209-2.2910.2551820.225108471146796.18
2.291-2.3840.259940.215106521110796.75
2.384-2.4890.2741850.219101221059997.245
2.489-2.6090.263780.21798431018297.437
2.609-2.7490.2451590.2199313968797.781
2.749-2.9130.212610.2228924915798.122
2.913-3.1110.2341110.2248400865498.348
3.111-3.3560.2461180.2267775799998.675
3.356-3.670.227770.2137243742498.599
3.67-4.0920.225900.1856580674098.961
4.092-4.7040.166930.1555831597099.229
4.704-5.7110.213470.185003507199.586
5.711-7.8740.304600.2173922398799.875
7.874-250.179270.1742387242199.711

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