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- PDB-3h6o: Activator-Bound Structure of Human Pyruvate Kinase M2 -

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Basic information

Entry
Database: PDB / ID: 3h6o
TitleActivator-Bound Structure of Human Pyruvate Kinase M2
ComponentsPyruvate kinase isozymes M1/M2
KeywordsTRANSFERASE / activator / Allosteric enzyme / Glycolysis / Kinase / Magnesium / Metal-binding / Phosphoprotein / 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-D8G / 1,6-di-O-phosphono-beta-D-fructofuranose / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 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
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / entity ...chem_comp / 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 / _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)242,21641
Polymers240,2004
Non-polymers2,01537
Water5,495305
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-111 kcal/mol
Surface area67090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.343, 155.690, 101.789
Angle α, β, γ (deg.)90.000, 108.040, 90.000
Int Tables number4
Space group name H-MP1211
Detailsauthors state that they have not independently confirmed the biological unit to be tetrameric.

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Components

#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
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#4: Chemical ChemComp-D8G / 6-(2-fluorobenzyl)-2,4-dimethyl-4,6-dihydro-5H-thieno[2',3':4,5]pyrrolo[2,3-d]pyridazin-5-one


Mass: 327.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14FN3OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.005M activator, pH 5.5, vapor diffusion, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 157058 / % possible obs: 97 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.077 / Χ2: 1.921 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.60.947156251.453196.8
2.07-2.153.60.701156911.502197.3
2.15-2.253.50.484157462.14197.4
2.25-2.373.60.443158521.892197.9
2.37-2.523.70.273158631.662198.3
2.52-2.713.70.184160201.736198.8
2.71-2.993.70.116160201.902199.1
2.99-3.423.70.069161222.143199.4
3.42-4.33.40.045137752.713184.9
4.3-203.80.034163442.197199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data scaling
RefinementStarting model: Direct placement of PDB entry 3GQY

3gqy


Resolution: 2→19.96 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.229 / SU B: 13.53 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic B-factors are residuals from TLS refinement. Phenix, coot, molprobity, prodrg were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1859 1.219 %thin shells (SFTOOLS)
Rwork0.247 ---
obs0.248 152479 94.23 %-
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: 33.749 Å2
Baniso -1Baniso -2Baniso -3
1--1.396 Å20 Å2-2.3 Å2
2--1.67 Å20 Å2
3----1.698 Å2
Refinement stepCycle: LAST / Resolution: 2→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14722 0 157 305 15184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0120.02215192
X-RAY DIFFRACTIONf_bond_other_d0.0020.0210132
X-RAY DIFFRACTIONf_angle_refined_deg1.1621.97620637
X-RAY DIFFRACTIONf_angle_other_deg0.862324701
X-RAY DIFFRACTIONf_dihedral_angle_1_deg5.40251976
X-RAY DIFFRACTIONf_dihedral_angle_2_deg32.83723.609604
X-RAY DIFFRACTIONf_dihedral_angle_3_deg13.054152486
X-RAY DIFFRACTIONf_dihedral_angle_4_deg16.51915118
X-RAY DIFFRACTIONf_chiral_restr0.0620.22383
X-RAY DIFFRACTIONf_gen_planes_refined0.0030.0217008
X-RAY DIFFRACTIONf_gen_planes_other0.0010.022934
X-RAY DIFFRACTIONf_nbd_refined0.1890.23234
X-RAY DIFFRACTIONf_nbd_other0.1860.210903
X-RAY DIFFRACTIONf_nbtor_refined0.1640.27429
X-RAY DIFFRACTIONf_nbtor_other0.0810.27642
X-RAY DIFFRACTIONf_xyhbond_nbd_refined0.1290.2494
X-RAY DIFFRACTIONf_symmetry_vdw_refined0.0210.21
X-RAY DIFFRACTIONf_symmetry_vdw_other0.2650.211
X-RAY DIFFRACTIONf_symmetry_hbond_refined0.1840.22
X-RAY DIFFRACTIONf_mcbond_it1.073210126
X-RAY DIFFRACTIONf_mcbond_other0.27324011
X-RAY DIFFRACTIONf_mcangle_it1.542315769
X-RAY DIFFRACTIONf_scbond_it1.02525806
X-RAY DIFFRACTIONf_scangle_it1.45734863
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 (%)
2-2.0510.3941260.327111851183295.597
2.051-2.1070.3951230.303109741152996.253
2.107-2.1670.291410.293107161124796.532
2.167-2.2330.3971010.40685391087879.426
2.233-2.3060.527990.40294301060089.896
2.306-2.3850.3181070.28197221023696.024
2.385-2.4740.2931150.2689562995297.237
2.474-2.5730.3181250.2699077942997.593
2.573-2.6860.3011200.2648831919097.399
2.686-2.8140.3281040.2618459876497.707
2.814-2.9630.3281070.2617998829897.674
2.963-3.1390.278900.2577647791797.726
3.139-3.350.336850.2537119739097.483
3.35-3.6090.312640.2414788694469.873
3.609-3.9410.261630.2315837641092.044
3.941-4.3850.213900.1925594582397.613
4.385-5.0230.216650.1765115519199.788
5.023-6.0570.279650.234352442599.819
6.057-8.1970.247430.2293468351599.886
8.197-19.960.226260.1892207224599.465
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)
11.5857-0.02790.04160.6509-0.0041.08890.04760.05240.060.02-0.05040.06920.0367-0.10710.0027-0.2158-0.0140.0298-0.0652-0.0025-0.1276-12.0284.117.221
21.32190.04270.09260.76340.04730.73140.03250.13380.1526-0.0893-0.0058-0.0237-0.03310.0648-0.0268-0.20020.00740.049-0.10890.0387-0.082721.01416.5550.81
30.74070.20640.37741.07530.40631.11620.09940.0163-0.13150.16250.0076-0.04260.41690.0932-0.10710.24820.019-0.055-0.11370.0127-0.087114.339-34.18632.21
40.88260.21550.04851.14530.12741.06380.0723-0.1551-0.01790.32030.0038-0.03780.17890.0794-0.07620.0580.0479-0.0627-0.0303-0.0378-0.117728.214-6.3950.554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 531
2X-RAY DIFFRACTION2B14 - 531
3X-RAY DIFFRACTION3C14 - 531
4X-RAY DIFFRACTION4D14 - 531

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