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- PDB-7l21: Pyruvate Kinase M2 mutant-N70D -

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Basic information

Entry
Database: PDB / ID: 7l21
TitlePyruvate Kinase M2 mutant-N70D
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / Glycolysis / allosteric regulation / kinase
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: 2.29 Å
AuthorsNandi, S. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CLP 1506181 United States
CitationJournal: Plos One / Year: 2023
Title: Identification of residues involved in allosteric signal transmission from amino acid binding site of pyruvate kinase muscle isoform 2.
Authors: Nandi, S. / Dey, M.
History
DepositionDec 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)243,02727
Polymers240,2044
Non-polymers2,82323
Water11,962664
1
D: Pyruvate kinase PKM
hetero molecules

C: Pyruvate kinase PKM
hetero molecules

B: Pyruvate kinase PKM
hetero molecules

A: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,02727
Polymers240,2044
Non-polymers2,82323
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
Buried area22250 Å2
ΔGint-127 kcal/mol
Surface area68780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.336, 158.303, 241.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 60051.086 Da / Num. of mol.: 4 / Mutation: N70D
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
#5: 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
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 683 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M bis tris propane, 22-24 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.29→63.811 Å / Num. all: 119675 / Num. obs: 119675 / % possible obs: 100 % / Redundancy: 15.1 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.133 / Rsym value: 0.124 / Net I/av σ(I): 6.1 / Net I/σ(I): 22.9 / Num. measured all: 1811940
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
2.29-2.41150.6031.3259830172650.1660.6470.6034.9100
2.41-2.5615.20.4681.7250351164450.1280.5020.4686.4100
2.56-2.7415.20.3452.2234284154070.0950.370.3459100
2.74-2.9615.20.2393.2219723144180.0660.2570.23913.2100
2.96-3.2415.20.1555202851133130.0420.1660.15519.7100
3.24-3.6215.20.0958.1182566120180.0260.1020.09530.2100
3.62-4.1815.20.0612.6161415106520.0160.0640.0643.6100
4.18-5.1215.10.04316.413689790440.0120.0460.04354.9100
5.12-7.24150.0514.410607370810.0140.0540.0549.8100
7.24-63.81114.40.0320.45795040320.0080.0320.0371.599.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B6U
Resolution: 2.29→63.81 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 5904 4.94 %
Rwork0.1834 113706 -
obs0.1856 119610 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.17 Å2 / Biso mean: 29.7191 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 2.29→63.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15287 0 119 664 16070
Biso mean--33.5 28.55 -
Num. residues----2052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.29-2.320.25291900.200736773867
2.32-2.340.29831790.212138183997
2.34-2.370.28252040.214337133917
2.37-2.40.26751860.211938194005
2.4-2.430.26111830.213337363919
2.43-2.470.24951980.214737793977
2.47-2.50.27172190.206737093928
2.5-2.540.26072010.198437503951
2.54-2.580.23162040.197837853989
2.58-2.620.25271760.190737763952
2.62-2.670.24591790.198837583937
2.67-2.720.25672250.196437743999
2.72-2.770.24142040.196337643968
2.77-2.820.24171850.197837523937
2.82-2.890.25691930.193637863979
2.89-2.950.26942140.199237563970
2.95-3.030.24242260.196337673993
3.03-3.110.25761860.196438073993
3.11-3.20.25412090.203837723981
3.2-3.30.23372060.185737663972
3.3-3.420.24541830.187237873970
3.42-3.560.21992060.181337803986
3.56-3.720.20861930.173238254018
3.72-3.920.20432010.165637983999
3.92-4.160.21081740.160538133987
4.16-4.480.17641830.147738434026
4.48-4.930.17392050.146938294034
4.93-5.650.22631890.178138534042
5.65-7.110.25062020.200938974099
7.11-63.810.18212010.16740174218

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