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- PDB-6wp5: Pyruvate Kinase M2 mutant-S37D -

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Basic information

Entry
Database: PDB / ID: 6wp5
TitlePyruvate Kinase M2 mutant-S37D
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / GLYCOLYSIS / GENE REGULATION / PHOSPHOTRANSFERASE
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
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: 2.17 Å
AuthorsNandi, S. / Razzaghi, M. / Srivastava, D. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CLP 1506181 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural basis for allosteric regulation of pyruvate kinase M2 by phosphorylation and acetylation.
Authors: Nandi, S. / Razzaghi, M. / Srivastava, D. / Dey, M.
History
DepositionApr 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Pyruvate kinase PKM
A: Pyruvate kinase PKM
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,74327
Polymers240,3124
Non-polymers2,43123
Water3,765209
1
A: Pyruvate kinase PKM
C: Pyruvate kinase PKM
hetero molecules

B: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,74327
Polymers240,3124
Non-polymers2,43123
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area21780 Å2
ΔGint-131 kcal/mol
Surface area64480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.625, 117.567, 109.965
Angle α, β, γ (deg.)90.000, 112.627, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein / Sugars , 2 types, 7 molecules BACD

#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: 60078.109 Da / Num. of mol.: 4 / Mutation: S37D
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
#6: 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.: 3 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 229 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaBr, 0.1 M Bis-Tris Propane, 16-20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786032 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786032 Å / Relative weight: 1
ReflectionResolution: 2.17→19.84 Å / Num. obs: 116911 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Rsym value: 0.069 / Net I/av σ(I): 10 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.17-2.293.80.5811.365318170880.3910.7670.5812.299.9
2.29-2.433.80.3871.961824161620.2610.5110.3873.499.9
2.43-2.593.80.2742.758031151810.1840.3610.2744.999.9
2.59-2.83.80.1774.253892141140.1190.2320.1777.499.9
2.8-3.073.80.1116.649296129840.0750.1460.11111.499.8
3.07-3.433.80.06610.944209117650.0450.0870.06617.999.7
3.43-3.963.70.04116.838191103840.0280.0540.04126.499.7
3.96-4.853.60.02922.23152287620.020.0380.02934.599.7
4.85-6.863.60.02823.12490268490.0190.0370.02835.399.7
6.86-19.843.60.0228.51316336220.0140.0270.0245.295.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
SCALA3.3.22data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B6U

6b6u


Resolution: 2.17→19.84 Å / SU ML: 0.3002 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2595 5771 4.94 %
Rwork0.2165 111075 -
obs0.2186 116846 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.83 Å2
Refinement stepCycle: LAST / Resolution: 2.17→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14184 0 100 209 14493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008414489
X-RAY DIFFRACTIONf_angle_d0.942819658
X-RAY DIFFRACTIONf_chiral_restr0.0622323
X-RAY DIFFRACTIONf_plane_restr0.00572566
X-RAY DIFFRACTIONf_dihedral_angle_d24.05785217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.190.35641760.33724X-RAY DIFFRACTION99.8
2.19-2.220.33281680.29223714X-RAY DIFFRACTION99.85
2.22-2.250.34211810.28983728X-RAY DIFFRACTION99.87
2.25-2.280.32562010.2813678X-RAY DIFFRACTION99.95
2.28-2.310.32072000.27583691X-RAY DIFFRACTION99.85
2.31-2.340.35821840.26293689X-RAY DIFFRACTION99.77
2.34-2.370.28321950.26173695X-RAY DIFFRACTION99.64
2.37-2.410.34471840.25723683X-RAY DIFFRACTION99.85
2.41-2.440.33571900.25543726X-RAY DIFFRACTION99.85
2.44-2.480.3362030.25373677X-RAY DIFFRACTION99.97
2.48-2.530.31091950.25153663X-RAY DIFFRACTION99.9
2.53-2.570.32051930.24173687X-RAY DIFFRACTION99.92
2.57-2.620.28362010.23123713X-RAY DIFFRACTION99.87
2.62-2.670.28351630.23073719X-RAY DIFFRACTION99.82
2.67-2.730.29341990.23423721X-RAY DIFFRACTION99.77
2.73-2.80.31971770.23263701X-RAY DIFFRACTION99.64
2.8-2.870.28611880.24473704X-RAY DIFFRACTION99.82
2.87-2.940.30851830.24853695X-RAY DIFFRACTION99.61
2.94-3.030.2931680.23233711X-RAY DIFFRACTION99.82
3.03-3.130.27782030.24313671X-RAY DIFFRACTION99.54
3.13-3.240.30711850.24013723X-RAY DIFFRACTION99.62
3.24-3.370.25651760.22453714X-RAY DIFFRACTION99.74
3.37-3.520.26982230.21343674X-RAY DIFFRACTION99.57
3.52-3.70.22641990.20113689X-RAY DIFFRACTION99.59
3.7-3.930.25741890.19213734X-RAY DIFFRACTION99.49
3.93-4.240.19642120.18293678X-RAY DIFFRACTION99.59
4.24-4.660.19191890.16363686X-RAY DIFFRACTION99.49
4.66-5.320.21722140.17863715X-RAY DIFFRACTION99.42
5.32-6.660.23612090.21793719X-RAY DIFFRACTION99.57
6.66-19.840.21122230.1743753X-RAY DIFFRACTION99.13

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