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- PDB-6wp4: Pyruvate Kinase M2 mutant-S37E -

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Basic information

Entry
Database: PDB / ID: 6wp4
TitlePyruvate Kinase M2 mutant-S37E
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / GLYCOLYSIS / GENE REGULATION / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / Pyruvate metabolism / positive regulation of cytoplasmic translation / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding ...pyruvate kinase / pyruvate kinase activity / histone H3T11 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 / cellular response to insulin stimulus / MHC class II protein complex binding / extracellular vesicle / : / protein tyrosine kinase activity / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / transcription coactivator activity / non-specific serine/threonine protein kinase / cilium / cadherin binding / intracellular membrane-bounded organelle / 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 / cytoplasm / cytosol
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
: / OXALATE ION / PHOSPHATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
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)243,61146
Polymers240,3694
Non-polymers3,24242
Water10,142563
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)243,61146
Polymers240,3694
Non-polymers3,24242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area25320 Å2
ΔGint-216 kcal/mol
Surface area69170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.167, 132.628, 110.128
Angle α, β, γ (deg.)90.000, 112.740, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 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: 60092.133 Da / Num. of mol.: 4 / Mutation: S37E
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

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Non-polymers , 7 types, 605 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M K2HPO4, 0.1 M HEPES, 20-24% 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: 1.000047 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000047 Å / Relative weight: 1
ReflectionResolution: 1.9→55.53 Å / Num. obs: 192145 / % possible obs: 98.2 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Rsym value: 0.066 / Net I/av σ(I): 9.7 / Net I/σ(I): 12.9
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
1.9-23.10.5081.581775262930.3390.6140.5082.192.1
2-2.123.60.3632.195453267980.2240.4270.3633.499.7
2.12-2.273.40.235385799252900.1510.280.2355.299.6
2.27-2.453.40.1485.279725235700.0940.1760.1487.699.8
2.45-2.693.70.109779290216870.0660.1280.10910.899.7
2.69-33.80.07110.874139196390.0420.0820.07116.299.8
3-3.473.70.04715.164253172250.0280.0540.04723.599.2
3.47-4.253.70.03518.353104143960.0220.0420.03531.798
4.25-6.013.70.03218.941334111130.0190.0370.03234.597.4
6.01-55.5273.70.02820.72268861340.0170.0330.02835.497

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALA3.3.22data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B6U

6b6u


Resolution: 1.9→55.53 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.22
RfactorNum. reflection% reflection
Rfree0.2208 9562 4.99 %
Rwork0.1885 --
obs0.1901 191611 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74 Å2 / Biso mean: 29.1646 Å2 / Biso min: 9.96 Å2
Refinement stepCycle: final / Resolution: 1.9→55.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15201 0 186 563 15950
Biso mean--36.96 30.55 -
Num. residues----2032
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.33762480.29755126537483
1.92-1.940.32382590.28795433569288
1.94-1.970.31112960.27095846614294
1.97-1.990.31323070.26136059636698
1.99-2.020.28933360.2446140647699
2.02-2.050.2643230.23596143646699
2.05-2.080.29193130.23316195650899
2.08-2.110.25553360.22086085642199
2.11-2.140.2553210.22136175649699
2.14-2.170.2662970.22176129642699
2.17-2.210.26693130.22086111642498
2.21-2.250.25993220.21326093641599
2.25-2.30.23633470.20761586505100
2.3-2.340.24473400.206260916431100
2.34-2.390.23533290.203362026531100
2.39-2.450.25233250.19946106643199
2.45-2.510.25583160.2026155647199
2.51-2.580.22673100.19496189649999
2.58-2.650.23383300.196961606490100
2.65-2.740.22183100.196461836493100
2.74-2.840.23143100.195562196529100
2.84-2.950.24473290.202561646493100
2.95-3.090.23433400.19186134647499
3.09-3.250.21983690.18836171654099
3.25-3.450.20633480.1816062641099
3.45-3.720.18363030.16566139644298
3.72-4.090.19033380.15466051638997
4.09-4.680.16613050.13856062636797
4.68-5.90.18333420.16036093643598
5.9-55.530.17943000.16436175647597

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