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- PDB-6b6u: Pyruvate Kinase M2 mutant - S437Y -

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Basic information

Entry
Database: PDB / ID: 6b6u
TitlePyruvate Kinase M2 mutant - S437Y
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / glycolysis / gene regulation / phosphotransferase
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, 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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / OXALATE ION / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSrivastava, D. / Dey, M.
CitationJournal: Biochemistry / Year: 2017
Title: Structural Investigation of a Dimeric Variant of Pyruvate Kinase Muscle Isoform 2.
Authors: Srivastava, D. / Razzaghi, M. / Henzl, M.T. / Dey, M.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,49621
Polymers114,8462
Non-polymers1,64919
Water18,5371029
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-85 kcal/mol
Surface area37800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.350, 93.610, 109.360
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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: 57423.145 Da / Num. of mol.: 2 / Mutation: S437Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase

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Non-polymers , 10 types, 1048 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1029 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Bis-Tris propane, Sodium thicynate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.2→28.985 Å / Num. obs: 297532 / % possible obs: 86.5 % / Observed criterion σ(I): -3 / Redundancy: 6.414 % / Biso Wilson estimate: 11.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.059 / Χ2: 1.095 / Net I/σ(I): 19.37 / Num. measured all: 1908333 / Scaling rejects: 961
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.233.5161.1640.81304772533886670.4671.37434.2
1.23-1.263.7631.021.054556524761121100.5571.19348.9
1.26-1.34.0770.8181.436218524025152530.6260.94463.5
1.3-1.344.4920.7281.768113623381180640.7030.82777.3
1.34-1.395.1280.5932.4410532922664205400.8040.66290.6
1.39-1.436.3640.5113.4313866321922217900.8830.55799.4
1.43-1.496.9990.3735.1214810821176211600.940.40399.9
1.49-1.556.8770.274713950720317202850.9660.29799.8
1.55-1.626.550.2039.0512785719547195190.9790.22199.9
1.62-1.76.7370.15112.2712554718675186360.9880.16499.8
1.7-1.797.1420.11417.0212650317752177130.9940.12399.8
1.79-1.97.5390.08522.9512679316828168190.9970.09299.9
1.9-2.037.5320.06131.6211889615792157850.9980.065100
2.03-2.197.5190.04539.6511088214754147470.9990.049100
2.19-2.47.5170.03746.7710191913569135590.9990.0499.9
2.4-2.687.5590.03251.679280612279122770.9990.035100
2.68-3.17.5410.02957.568147210812108040.9990.03199.9
3.1-3.797.440.02662.0868184919791650.9990.02899.7
3.79-5.377.3020.02364.3450934711069750.9990.02598.1
5.37-28.9856.9790.02462.5825570399136640.9990.02691.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GR4

3gr4


Resolution: 1.35→28.985 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1494 11963 4.99 %
Rwork0.1303 227621 -
obs0.1312 239584 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.37 Å2 / Biso mean: 18.2865 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.35→28.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7886 0 184 1029 9099
Biso mean--30.69 24.81 -
Num. residues----1035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098386
X-RAY DIFFRACTIONf_angle_d0.9611345
X-RAY DIFFRACTIONf_chiral_restr0.0771306
X-RAY DIFFRACTIONf_plane_restr0.0061475
X-RAY DIFFRACTIONf_dihedral_angle_d20.9293204
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 (%)
1.35-1.36530.22173670.196847721489
1.3653-1.38140.21273770.17787105748294
1.3814-1.39830.20163750.16597503787898
1.3983-1.41590.19824100.155475998009100
1.4159-1.43460.19193920.150976388030100
1.4346-1.45420.18743730.144376628035100
1.4542-1.4750.17773740.134276748048100
1.475-1.4970.17013850.133575957980100
1.497-1.52040.16273930.127376198012100
1.5204-1.54530.16223700.124876648034100
1.5453-1.5720.16533840.12376678051100
1.572-1.60060.15833990.116275997998100
1.6006-1.63130.14993790.119276538032100
1.6313-1.66460.15154000.117776328032100
1.6646-1.70080.14983930.116575927985100
1.7008-1.74040.13864130.117476718084100
1.7404-1.78390.13933850.116776308015100
1.7839-1.83210.14854040.117976548058100
1.8321-1.8860.1484050.123676388043100
1.886-1.94690.15564290.11776458074100
1.9469-2.01650.14314370.121676088045100
2.0165-2.09720.13353950.116376268021100
2.0972-2.19260.13874470.118976538100100
2.1926-2.30820.13624050.116876358040100
2.3082-2.45270.14213780.122277198097100
2.4527-2.6420.14844470.12676428089100
2.642-2.90760.14553920.132577018093100
2.9076-3.32780.14354270.137776618088100
3.3278-4.19070.13154280.13087656808499
4.1907-28.99130.15734000.15447433783395

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