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- PDB-5x0i: Crystal structure of PKM2 R399E mutant complexed with FBP and serine -

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Basic information

Entry
Database: PDB / ID: 5x0i
TitleCrystal structure of PKM2 R399E mutant complexed with FBP and serine
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / pyruvate kinase / glycolysis
Function / homology
Function and homology information


pyruvate kinase / pyruvate 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 ...pyruvate kinase / pyruvate 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 / cilium / cellular response to insulin stimulus / MHC class II protein complex binding / extracellular vesicle / protein tyrosine kinase activity / collagen-containing extracellular matrix / secretory granule lumen / vesicle / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / ficolin-1-rich granule lumen / transcription coactivator activity / histone H3T11 kinase 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
Pyruvate kinase, C-terminal domain / Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / 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, active site / Pyruvate kinase active site signature. / Pyruvate Kinase; Chain: A, domain 1 / 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 / : / PYRUVIC ACID / SERINE / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWang, W.C. / Chen, T.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
NHRINHRI-EX105-10517BI Taiwan
CitationJournal: Commun Biol / Year: 2019
Title: Mutations in the PKM2 exon-10 region are associated with reduced allostery and increased nuclear translocation.
Authors: Chen, T.J. / Wang, H.J. / Liu, J.S. / Cheng, H.H. / Hsu, S.C. / Wu, M.C. / Lu, C.H. / Wu, Y.F. / Wu, J.W. / Liu, Y.Y. / Kung, H.J. / Wang, W.C.
History
DepositionJan 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)243,02724
Polymers240,6414
Non-polymers2,38720
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22150 Å2
ΔGint-133 kcal/mol
Surface area71850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.601, 137.875, 149.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / p58


Mass: 60160.164 Da / Num. of mol.: 4 / Mutation: R399E
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
#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 , 5 types, 61 molecules

#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: KCl, Tris, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.64→30 Å / Num. obs: 72242 / % possible obs: 99.9 % / Redundancy: 4.8 % / Net I/σ(I): 16.59
Reflection shellResolution: 2.64→2.73 Å / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B2D

4b2d


Resolution: 2.64→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.302 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 1.002 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21844 3614 5.1 %RANDOM
Rwork0.18 ---
obs0.18194 67778 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2--1.36 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15838 0 140 45 16023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01916205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215961
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.97821910
X-RAY DIFFRACTIONr_angle_other_deg0.75336767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48252064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.16524.063667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53152909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.89915120
X-RAY DIFFRACTIONr_chiral_restr0.0830.22527
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023420
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_it3.3354.0478283
X-RAY DIFFRACTIONr_mcbond_other3.3354.0468282
X-RAY DIFFRACTIONr_mcangle_it5.0856.06510338
X-RAY DIFFRACTIONr_mcangle_other5.0856.06510339
X-RAY DIFFRACTIONr_scbond_it4.2734.5697922
X-RAY DIFFRACTIONr_scbond_other4.2734.5697921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7666.62511572
X-RAY DIFFRACTIONr_long_range_B_refined8.71531.84817674
X-RAY DIFFRACTIONr_long_range_B_other8.71531.84817675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 282 -
Rwork0.255 4880 -
obs--99.94 %

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