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- PDB-3g2g: S437Y Mutant of human muscle pyruvate kinase, isoform M2 -

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Basic information

Entry
Database: PDB / ID: 3g2g
TitleS437Y Mutant of human muscle pyruvate kinase, isoform M2
ComponentsPyruvate kinase isozymes M1/M2
KeywordsTRANSFERASE / Structural Genomics Consortium (SGC) / single nucleotide polymorphism / SNP / mutation / Acetylation / Allosteric enzyme / Alternative splicing / Glycolysis / Kinase / Magnesium / Metal-binding / Phosphoprotein / Polymorphism / Pyruvate
Function / homology
Function and homology information


positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / canonical glycolysis / Glycolysis / positive regulation of sprouting angiogenesis / potassium ion binding / rough endoplasmic reticulum ...positive regulation of cytoplasmic translation / pyruvate kinase / pyruvate kinase activity / histone H3T11 kinase activity / programmed cell death / 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 / secretory granule lumen / collagen-containing extracellular matrix / 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 / cytoplasm / cytosol
Similarity search - Function
PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 ...PK beta-barrel domain-like / M1 Pyruvate Kinase; Domain 3 / 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 / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHong, B. / Dimov, S. / Allali-Hassani, A. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, c. / Weigelt, J. / Bochkarev, A. ...Hong, B. / Dimov, S. / Allali-Hassani, A. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, c. / Weigelt, J. / Bochkarev, A. / Vedadi, M. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: S437Y Mutant of human muscle pyruvate kinase, isoform M2
Authors: Allali-Hassani, A. / Hong, B. / Dimov, S. / Tempel, W. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, c. / Weigelt, J. / Bochkarev, A. / Park, H. / Vedadi, M.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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 isozymes M1/M2
B: Pyruvate kinase isozymes M1/M2
C: Pyruvate kinase isozymes M1/M2
D: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,19748
Polymers232,9484
Non-polymers1,24944
Water8,377465
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17660 Å2
ΔGint-261 kcal/mol
Surface area67050 Å2
MethodPISA
2
A: Pyruvate kinase isozymes M1/M2
B: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,95423
Polymers116,4742
Non-polymers48021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-94 kcal/mol
Surface area34640 Å2
MethodPISA
3
C: Pyruvate kinase isozymes M1/M2
D: Pyruvate kinase isozymes M1/M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,24325
Polymers116,4742
Non-polymers76923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-140 kcal/mol
Surface area36460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.546, 137.885, 155.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Pyruvate kinase isozymes M1/M2 / Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / ...Pyruvate kinase muscle isozyme / Pyruvate kinase 2/3 / Cytosolic thyroid hormone-binding protein / CTHBP / THBP1


Mass: 58237.086 Da / Num. of mol.: 4 / Mutation: S437Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM2, PK2, PK3, PKM / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P14618, pyruvate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG-1500, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. obs: 153815 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Χ2: 1.547 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0770.999151171.46399.1
2.07-2.1570.721151551.52499.3
2.15-2.257.10.53152011.5699.4
2.25-2.377.20.387152291.58299.6
2.37-2.527.30.289153371.58899.8
2.52-2.717.30.206153551.699.9
2.71-2.997.30.128153681.621100
2.99-3.427.40.072155061.603100
3.42-4.37.40.041155321.552100
4.3-227.30.029160151.374100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1zjh

1zjh


Resolution: 2→21.957 Å / FOM work R set: 0.799
RfactorNum. reflection% reflectionSelection details
Rfree0.26 4033 1.37 %thin shells (sftools)
Rwork0.227 ---
obs0.227 152544 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.545 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 80.75 Å2 / Biso mean: 33.44 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1--3.061 Å2-0 Å20 Å2
2---2.016 Å20 Å2
3---5.076 Å2
Refinement stepCycle: LAST / Resolution: 2→21.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14604 0 96 465 15165

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