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- PDB-4rpp: crystal structure of PKM2-K422R mutant bound with FBP -

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Basic information

Entry
Database: PDB / ID: 4rpp
Titlecrystal structure of PKM2-K422R mutant bound with FBP
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / PKM2
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 / 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 / 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, 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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsWang, P. / Sun, C. / Zhu, T. / Xu, Y.
CitationJournal: Protein Cell / Year: 2015
Title: Structural insight into mechanisms for dynamic regulation of PKM2.
Authors: Wang, P. / Sun, C. / Zhu, T. / Xu, Y.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Structure summary
Revision 1.2Jul 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
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 1.3Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity.formula_weight / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type

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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)234,9588
Polymers233,5974
Non-polymers1,3604
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17500 Å2
ΔGint-91 kcal/mol
Surface area58460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.674, 152.554, 97.676
Angle α, β, γ (deg.)90.00, 104.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyruvate kinase PKM / Pyruvate kinase muscle isozyme / Threonine-protein kinase PKM2Tumor M2-PK / Tyrosine-protein kinase PKM2


Mass: 58399.281 Da / Num. of mol.: 4 / Mutation: K422R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, PKM2 / Production host: Escherichia coli (E. coli) / 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 / Fructose 1,6-bisphosphate


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Sodium chloride, 0.1M BIS-TRIS propane pH 9.0, 25% PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.585→50 Å / Num. all: 70893 / Num. obs: 70651 / % possible obs: 99 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.585→38.313 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 37.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.308 3461 4.9 %
Rwork0.2736 --
obs0.2753 70650 97.56 %
all-70893 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.585→38.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12486 0 80 30 12596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312776
X-RAY DIFFRACTIONf_angle_d0.76517278
X-RAY DIFFRACTIONf_dihedral_angle_d14.7854862
X-RAY DIFFRACTIONf_chiral_restr0.0291982
X-RAY DIFFRACTIONf_plane_restr0.0042242
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.585-2.61990.3794950.3583199773
2.6199-2.65730.40631430.34832697100
2.6573-2.6970.40081200.35962796100
2.697-2.73910.42271460.35812725100
2.7391-2.7840.36621450.35462739100
2.784-2.8320.38171510.33562738100
2.832-2.88350.34251460.34332713100
2.8835-2.93890.40141520.32442739100
2.9389-2.99890.3391300.3353274199
2.9989-3.06410.39681440.3239272399
3.0641-3.13530.44231340.34152761100
3.1353-3.21370.38051400.33232704100
3.2137-3.30050.34811440.3245274799
3.3005-3.39760.42281400.32092754100
3.3976-3.50720.35821420.29562716100
3.5072-3.63240.32891420.27872754100
3.6324-3.77780.32361220.27472753100
3.7778-3.94950.2771610.2655273599
3.9495-4.15750.30261420.2654270699
4.1575-4.41760.27181340.2459272398
4.4176-4.75820.2481520.22264997
4.7582-5.23590.27051290.2365274398
5.2359-5.99110.28631340.2599273699
5.9911-7.53870.2631440.2572277099
7.5387-38.31760.27341290.2393233083
Refinement TLS params.Method: refined / Origin x: 41.9839 Å / Origin y: 7.0591 Å / Origin z: 69.8567 Å
111213212223313233
T0.6662 Å20.0951 Å2-0.0036 Å2-0.4804 Å2-0.0362 Å2--0.4095 Å2
L1.1689 °2-0.1767 °20.3251 °2-0.5193 °2-0.1441 °2--0.5584 °2
S0.268 Å °0.2337 Å °-0.0272 Å °0.0551 Å °-0.1225 Å °-0.0219 Å °0.3744 Å °0.1411 Å °-0.1267 Å °
Refinement TLS groupSelection details: all

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