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- PDB-8hmr: Crystal Structure of PKM2 mutant L144P -

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Basic information

Entry
Database: PDB / ID: 8hmr
TitleCrystal Structure of PKM2 mutant L144P
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / PKM2 / Hydroxylation / Kinase / Glycolysis / Tumour Promoting / Warburg Effect
Function / homology
Function and homology information


programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...programmed cell death / pyruvate kinase / pyruvate kinase activity / positive regulation of cytoplasmic translation / histone H3T11 kinase activity / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum / glycolytic process / non-specific protein-tyrosine kinase / cilium / cellular response to insulin stimulus / extracellular vesicle / MHC class II protein complex binding / collagen-containing extracellular matrix / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cadherin binding / phosphorylation / 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
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
1,6-di-O-phosphono-beta-D-fructofuranose / OXALATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsUpadhyay, S. / Kumar, A. / Patel, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/RLF/Re-entry/57/2012 India
CitationJournal: To Be Published
Title: Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2
Authors: Upadhyay, S. / Kumar, A. / Patel, A.K.
History
DepositionDec 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: 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)242,62318
Polymers240,6894
Non-polymers1,93414
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20950 Å2
ΔGint-142 kcal/mol
Surface area69860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.400, 151.769, 89.850
Angle α, β, γ (deg.)90.00, 100.59, 90.00
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 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: 60172.203 Da / Num. of mol.: 4 / Mutation: L144P
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
#3: 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 / Fructose 1,6-bisphosphate


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 29 molecules

#2: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium chloride, 0.1 M HEPES pH7.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→44.16 Å / Num. obs: 63685 / % possible obs: 98 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.054 / Rrim(I) all: 0.109 / Χ2: 1.03 / Net I/σ(I): 9 / Num. measured all: 261074
Reflection shellResolution: 2.6→2.66 Å / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.847 / Num. measured all: 19161 / Num. unique obs: 4557 / CC1/2: 0.77 / Rpim(I) all: 0.469 / Rrim(I) all: 0.97 / Χ2: 0.9 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GR4

3gr4


Resolution: 2.6→42.01 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.914 / SU B: 56.658 / SU ML: 0.484 / Cross valid method: THROUGHOUT / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29473 3197 5 %RANDOM
Rwork0.26295 ---
obs0.26455 60264 97.6 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.345 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å2-0 Å2-2.35 Å2
2---1.77 Å2-0 Å2
3---5.11 Å2
Refinement stepCycle: 1 / Resolution: 2.6→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15411 0 116 19 15546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01215764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.64721349
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54352022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.5375125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.143102719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.22489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211569
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2382.4948124
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6263.73410134
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8392.6537640
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.47349.06267988
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 228 -
Rwork0.382 4552 -
obs--99.85 %
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)
12.0597-0.2850.14442.859-0.31861.16420.24580.22360.0064-0.3823-0.1150.45720.1924-0.1298-0.13080.50260.0696-0.23950.8557-0.0220.1534-10.4966.50934.436
22.38650.30290.14812.219-0.0931.6650.1190.52090.2824-0.6568-0.1085-0.28840.01530.1419-0.01050.5370.16780.03960.84390.12820.106322.1517.1506-1.6667
31.3871-0.54630.28252.5148-0.28311.06760.1240.0837-0.3917-0.18720.00760.27640.33490.1079-0.13160.94630.0557-0.27630.7682-0.00470.178218.23-35.213632.6064
41.4149-0.3349-0.17313.8041-0.58411.6311-0.0741-0.24540.19741.11680.0373-0.49660.16830.35310.03680.87330.0946-0.37250.7705-0.03430.19132.539-7.069448.2552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 115
2X-RAY DIFFRACTION1A116 - 220
3X-RAY DIFFRACTION1A221 - 602
4X-RAY DIFFRACTION2B15 - 115
5X-RAY DIFFRACTION2B116 - 220
6X-RAY DIFFRACTION2B221 - 602
7X-RAY DIFFRACTION3C15 - 115
8X-RAY DIFFRACTION3C116 - 220
9X-RAY DIFFRACTION3C221 - 602
10X-RAY DIFFRACTION4D15 - 115
11X-RAY DIFFRACTION4D116 - 220
12X-RAY DIFFRACTION4D221 - 602

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