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- PDB-9hib: K115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2) -

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Basic information

Entry
Database: PDB / ID: 9hib
TitleK115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2)
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / acetylation / post-translational modification / glycolysis / genetic code expansion / acetylated lysine / metabolism
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / 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 / cellular response to insulin stimulus / MHC class II protein complex binding / extracellular vesicle / : / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cilium / cadherin binding / intracellular membrane-bounded organelle / 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 / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
: / SUCCINIC ACID / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPavlenko, D. / Nudelman, H. / Shahar, A. / Arbely, E.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)678461European Union
Israel Science Foundation1769/20 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Isoform-specific regulation of PKM by acetylation
Authors: Pavlenko, D. / Tamargo-Azpilicueta, J. / Ankri, Y. / Nudelman, H. / Shahar, A. / Diez-Moreno, I. / Arbely, E.
History
DepositionNov 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase PKM
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,96223
Polymers235,5474
Non-polymers1,41519
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21430 Å2
ΔGint-47 kcal/mol
Surface area72400 Å2
Unit cell
Length a, b, c (Å)81.536, 154.783, 100.700
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate kinase PKM / Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate ...Cytosolic thyroid hormone-binding protein / CTHBP / Opa-interacting protein 3 / OIP-3 / Pyruvate kinase 2/3 / Pyruvate kinase muscle isozyme / Threonine-protein kinase PKM2 / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / Tyrosine-protein kinase PKM2 / p58


Mass: 58886.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P14618, pyruvate kinase, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

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Non-polymers , 7 types, 286 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 5% Tacsimate 0.1M Hepes pH 6.8 12.14% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.17→81.64 Å / Num. obs: 125584 / % possible obs: 99.79 % / Redundancy: 7.1 % / CC1/2: 0.973 / Net I/σ(I): 12.9
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 12530 / CC1/2: 0.347

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→81.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 20.244 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26503 6232 5 %RANDOM
Rwork0.22299 ---
obs0.22505 119349 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.921 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å2-1.16 Å2
2---1.84 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.17→81.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15640 0 90 267 15997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01215996
X-RAY DIFFRACTIONr_bond_other_d0.0030.01615724
X-RAY DIFFRACTIONr_angle_refined_deg2.1421.82521581
X-RAY DIFFRACTIONr_angle_other_deg0.8341.76936239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81552035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.3665129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.235102857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1090.22479
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218744
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023460
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9591.8398150
X-RAY DIFFRACTIONr_mcbond_other1.9591.8398150
X-RAY DIFFRACTIONr_mcangle_it3.1743.30610175
X-RAY DIFFRACTIONr_mcangle_other3.1743.30710176
X-RAY DIFFRACTIONr_scbond_it2.482.0427846
X-RAY DIFFRACTIONr_scbond_other2.482.0427847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7943.6811405
X-RAY DIFFRACTIONr_long_range_B_refined6.95716.9316930
X-RAY DIFFRACTIONr_long_range_B_other6.95516.8716888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 446 -
Rwork0.353 8811 -
obs--99.78 %
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)
11.25680.1199-0.2171.2791-0.21321.79530.078-0.2332-0.07980.3519-0.0037-0.03030.24410.1134-0.07440.43910.0021-0.2470.6076-0.00910.429868.9748-27.70451.2811
21.9571-0.1762-0.2341.33610.19991.80550.12220.06240.09430.0133-0.15850.16340.0899-0.20850.03630.0417-0.0229-0.08710.5201-0.02930.372928.755-14.0677.3505
31.56210.1890.16441.33080.04541.40980.12920.21550.2534-0.1824-0.0734-0.1521-0.03440.108-0.05580.05390.0615-0.01290.49490.07170.507561.7539-4.65880.1245
41.03480.19070.24781.26260.09021.2209-0.0118-0.003-0.52390.14980.0403-0.16080.52860.1329-0.02850.8219-0.0468-0.17830.5760.03290.679157.7778-55.810633.2517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 602
2X-RAY DIFFRACTION2B14 - 604
3X-RAY DIFFRACTION3C14 - 615
4X-RAY DIFFRACTION4D14 - 601

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