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- PDB-8hms: Crystal Structure of PKM2 mutant C474S -

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Basic information

Entry
Database: PDB / ID: 8hms
TitleCrystal Structure of PKM2 mutant C474S
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / PKM2 / Hydroxylation / Kinase / Glycolysis / Tumour Promoting / Warburg Effect
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: 2.1 Å
AuthorsUpadhyay, S. / Kumar, A. / Patel, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/RLF/Re-entry/57/2012 India
CitationJournal: To Be Published
Title: Structural and mechanistic insights into cancer patient-derived mutations in Pyruvate Kinase muscle isoform 2
Authors: Upadhyay, S. / Kumar, A. / Patel, A.K.
History
DepositionDec 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)242,89326
Polymers240,6894
Non-polymers2,20522
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.733, 134.584, 148.528
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 15 or (resid 16...
d_2ens_1(chain "B" and ((resid 14 and (name N or name...
d_3ens_1(chain "C" and ((resid 14 and (name N or name...
d_4ens_1(chain "D" and ((resid 14 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNLYSA1 - 122
d_12ens_1ASPASNA134 - 144
d_13ens_1GLUGLNA150 - 168
d_14ens_1THRCYSA176 - 404
d_15ens_1SERPROA406 - 512
d_21ens_1GLNGLYG2 - 114
d_22ens_1GLULYSG121 - 129
d_23ens_1ASPASNG141 - 151
d_24ens_1GLUGLNG157 - 175
d_25ens_1THRCYSG183 - 411
d_26ens_1SERPROG413 - 519
d_31ens_1GLNGLYL2 - 114
d_32ens_1GLULYSL121 - 129
d_33ens_1ASPASNL141 - 151
d_34ens_1GLUGLNL157 - 175
d_35ens_1THRCYSL183 - 411
d_36ens_1SERPROL413 - 519
d_41ens_1GLNGLYR1 - 113
d_42ens_1GLUCYSR118 - 385
d_43ens_1SERPROR387 - 493

NCS oper:
IDCodeMatrixVector
1given(-0.765793884771, 0.524503019587, 0.372097176141), (0.473953813479, 0.0692375800219, 0.877823410602), (0.434657921516, 0.848588675365, -0.301611921692)-82.3104772311, 46.2813417184, -9.09246612614
2given(-0.404198632869, -0.761893633974, 0.506104293301), (-0.690900381835, -0.108282457654, -0.714794775963), (0.599399806112, -0.638586720716, -0.482624981283)-57.4157159742, -48.3367015277, -0.535467157687
3given(0.0824794816773, 0.189808316138, -0.978350621315), (0.2183760503, -0.961279817813, -0.16808632461), (-0.972372889255, -0.199784671561, -0.120735451512)-67.9134821847, 12.774214729, -72.1332105035

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Components

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Protein / Sugars , 2 types, 7 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 / Threonine-protein kinase PKM2 / Thyroid hormone-binding protein 1 / THBP1 / Tumor M2-PK / Tyrosine-protein kinase PKM2 / p58


Mass: 60172.188 Da / Num. of mol.: 4 / Mutation: C474S
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, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase
#2: 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.: 3 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 439 molecules

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


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium citrate tribasic dihydrate 0.1 M Bis-Tris propane pH8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9778 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.1→46.85 Å / Num. obs: 115815 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 41.74 Å2 / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 5659 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GR4

3gr4


Resolution: 2.1→46.85 Å / SU ML: 0.2474 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 5845 5.06 %
Rwork0.2037 109668 -
obs0.2054 115513 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15216 0 135 420 15771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415582
X-RAY DIFFRACTIONf_angle_d0.659421118
X-RAY DIFFRACTIONf_chiral_restr0.08332466
X-RAY DIFFRACTIONf_plane_restr0.00762757
X-RAY DIFFRACTIONf_dihedral_angle_d6.30752208
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.02942102481
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.03905041259
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.04688672874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32561990.27583607X-RAY DIFFRACTION99.92
2.12-2.150.30051720.27493679X-RAY DIFFRACTION100
2.15-2.180.33971780.27743602X-RAY DIFFRACTION100
2.18-2.20.3131950.26253624X-RAY DIFFRACTION99.97
2.2-2.230.28842060.25353604X-RAY DIFFRACTION99.95
2.23-2.260.28291890.25153609X-RAY DIFFRACTION99.92
2.26-2.290.27592020.2553649X-RAY DIFFRACTION99.95
2.29-2.330.30061910.24293621X-RAY DIFFRACTION99.82
2.33-2.370.27772100.24483600X-RAY DIFFRACTION99.9
2.37-2.40.26921920.23993658X-RAY DIFFRACTION99.9
2.4-2.450.28511820.24733632X-RAY DIFFRACTION99.95
2.45-2.490.29831640.24823659X-RAY DIFFRACTION99.9
2.49-2.540.26551870.24323650X-RAY DIFFRACTION99.87
2.54-2.590.30971910.25863608X-RAY DIFFRACTION99.87
2.59-2.650.28631920.24823647X-RAY DIFFRACTION99.77
2.65-2.710.28662140.24433616X-RAY DIFFRACTION99.58
2.71-2.770.28481770.2343625X-RAY DIFFRACTION99.79
2.78-2.850.2961880.23543654X-RAY DIFFRACTION99.74
2.85-2.930.2891950.23473666X-RAY DIFFRACTION99.61
2.93-3.030.25422200.22543604X-RAY DIFFRACTION99.77
3.03-3.140.26362210.22163618X-RAY DIFFRACTION99.61
3.14-3.260.22181940.21483652X-RAY DIFFRACTION99.59
3.26-3.410.24231910.2043679X-RAY DIFFRACTION99.67
3.41-3.590.22092010.19623647X-RAY DIFFRACTION99.56
3.59-3.820.23431800.18363692X-RAY DIFFRACTION99.46
3.82-4.110.19992070.17263667X-RAY DIFFRACTION99.44
4.11-4.520.1951920.16353710X-RAY DIFFRACTION99.69
4.52-5.180.1992100.16683716X-RAY DIFFRACTION99.8
5.18-6.520.24531920.20873780X-RAY DIFFRACTION99.95
6.52-46.850.19062130.16713893X-RAY DIFFRACTION99.11
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.88670787411-0.638977956357-0.01426478766912.90367070169-0.5174619201961.44554347786-0.317761748068-0.464031136061-0.436114520144-0.1250138717110.0258898589519-0.6291568144210.1365671972550.4506568501270.2210320669560.3527775376030.05218732128250.1174643179660.4993103751320.2455741630140.604016265545-18.0577559338-4.58192967439-32.8210778999
22.33715153112-0.757760658817-0.406909083822.69466882018-0.9941708463151.38942899221-0.4092415054070.62518942899-0.15543360315-1.65782850624-0.527300709395-0.4698775533060.850707152833-0.1774028776160.3953523324530.8788205277880.02829819724080.3917735723510.734317472574-0.01508649750240.846476401371-24.9139967172-9.85389617333-59.8428753616
32.46846527910.333491396463-0.5454040249062.29848896243-0.1732890391951.70385434889-0.443894052625-0.178719449575-0.855169437852-0.2806118422590.00230021927973-0.2685050722240.3727476941570.2081207541870.289240634450.4061261630980.06583030855290.202964667610.2514370574230.08976467672150.554187084176-28.716100291-8.78430921424-39.347648604
41.747139357160.0335581783262-0.2508081654262.60442447521-0.2141249773272.390913761420.118553857169-0.0727082385988-0.0378426184339-0.0162880822933-0.28554741426-0.7391230312420.05842047623050.185511771690.1007762470870.3140434864220.09744960805770.08932117336940.4557141595470.2339310140930.61822411378-24.7439519435-15.9305868001-16.0213253877
52.3659946853-0.9168439029990.1628901334424.45201401004-2.23997847532.66998563962-0.03156303337520.2117762520830.177111699472-0.506010784595-0.0651656562747-0.1299754368630.1971967669510.08487231544040.08715122682680.3379964080390.05110673607660.01547386651220.276742498202-0.02435165710030.249207070753-37.871501457118.6050459137-50.5020735043
65.270545508320.8680990115721.055727021242.28866106970.09898044582471.18161576465-0.2691696387620.4833685821660.68415237858-0.283909162883-0.0691617580014-0.796174203939-0.0911974260940.5027304648970.265868459990.4479114104420.03688395468550.08341536748170.5184701093750.2149612948250.81848147933-19.635331799129.6769804435-45.7528285785
78.65578189491-0.77320815290.3884947271374.11677627561-0.596692486541.95864853909-0.0592880649388-0.5121432880440.2572661665550.371751627519-0.389206373829-0.8225929851170.2202446932530.4647085482680.3058331710040.59036744824-0.0303201846942-0.06365968056370.8348063556350.1643928153970.931061428649-6.7056310658828.4307979571-34.2085758199
82.41886310991-0.820289001108-0.07265588781351.83325159722-0.6721986907241.01486621002-0.0887373096085-0.03314021118520.33026608791-0.03283104403830.0598294458906-0.124420716503-0.08950401727910.01093408231120.02886306321410.35042051204-0.0053886060282-0.04851814113860.229846477889-0.008775342676720.262655817519-42.917585561823.0044487315-40.8521833747
91.88686254741-0.4523650377791.493640796613.23499506566-2.262602896474.288340541880.0299127352458-0.285462754004-0.1301957201390.116973432623-0.02784979542720.009579450157360.427965239909-0.06853405854570.01483216353260.2915096196840.01254122221250.01656445064750.3319563492490.04259223070120.284875095527-62.5470384952-14.11001145894.7375040766
102.64196746592-1.50391357053-0.5703444576182.526293429260.6825908790932.793910763040.00171168422095-0.4935484542990.2686324727030.726133438541-0.1886986587020.503869613021-0.44451227947-0.7371147339750.1211061880.905127680649-0.02944370292360.1411386039910.87438498415-0.1332962187650.477821977433-73.66460228656.2957622282422.076207232
111.895381631370.01356406552550.6714441832722.32945328866-0.5004789408621.82620524348-0.0378816814061-0.4211736404380.2180208062920.477131263321-0.0782813224823-0.180069788207-0.1620866648390.1135594145480.1102084594450.3938946267640.0123145436579-0.05221506951680.398860837562-0.0212256975720.193476121886-59.2229036767-1.119145309746.31453622056
122.14552247009-0.563535958056-0.5452083679953.064936968720.2381222763752.08913745269-0.0285741823179-0.391093155747-0.191794514910.173262283315-0.0259527589956-0.3920962070190.2431062046820.337556403120.03908076016050.3138439566860.0684852367643-0.03750657139150.4239011183910.1426406799050.315795944543-42.6830347458-18.67471273370.276029641157
136.69393458605-0.9583026722641.953443235211.85800151151-1.04051581512.49225261224-0.00892949281439-0.1553717812330.7334487148740.141616427390.1868153953340.359143274654-0.161979414399-0.462098464862-0.1559703498680.4350172664430.09052697046240.07390898885920.359463545680.06466921939990.433538043225-81.46520520611.5090347456-10.618066345
142.198150734960.129131550836-0.1619652677692.77987759307-2.232199116561.50476314484-0.0801907612848-0.260725384823-0.116263919290.04624629464320.4396054013620.5772888926740.0794549344891-0.432595288112-0.3655766006330.391203334326-0.003944645614420.0228017307190.5545995699850.166874131960.457760885033-95.2899756294-13.2912159006-4.57492313953
152.391473280830.1473274457440.506757709172.13557690702-0.6805642307341.42605424543-0.04891053680140.1486827465560.124276442933-0.199927561820.215951890520.4074652208210.275023116835-0.371201726138-0.1425813788830.276408579377-0.0468633134311-0.03179068511760.3624852551610.09100111539440.283635983787-82.7627521706-2.73914729232-15.4121689566
162.28460722331.20317617844-0.224753798790.996083572349-0.4447165337482.24062593651-0.2442595885990.2756574302950.633249208485-0.1144555698710.3867091978730.565394695859-0.10454542726-0.384007005657-0.1354570816870.3291929969920.0164179340436-0.08701218029620.3753711566950.1865304002950.560035465971-74.164049370816.6274440633-27.5930377873
172.128331328190.182904984528-2.284814119795.265874945690.8878747173272.68881100705-0.2312503372950.2569120934250.540992865191-0.257689538669-0.06555310782520.890035120413-0.883399069804-0.4729189360410.2453430625260.4151232542940.0417816984519-0.08956604354790.4756093843550.2106904406920.674956179064-71.950186195424.6436952435-29.1425735043
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 14 through 98 )DR14 - 981 - 85
22chain 'D' and (resid 99 through 222 )DR99 - 22286 - 184
33chain 'D' and (resid 223 through 407 )DR223 - 407185 - 369
44chain 'D' and (resid 408 through 531 )DR408 - 531370 - 493
55chain 'A' and (resid 14 through 98 )AA14 - 981 - 85
66chain 'A' and (resid 99 through 148 )AA99 - 14886 - 129
77chain 'A' and (resid 149 through 222 )AA149 - 222130 - 203
88chain 'A' and (resid 223 through 531 )AA223 - 531204 - 512
99chain 'B' and (resid 13 through 98 )BG13 - 981 - 86
1010chain 'B' and (resid 99 through 222 )BG99 - 22287 - 210
1111chain 'B' and (resid 223 through 407 )BG223 - 407211 - 395
1212chain 'B' and (resid 408 through 531 )BG408 - 531396 - 519
1313chain 'C' and (resid 13 through 98 )CL13 - 981 - 86
1414chain 'C' and (resid 99 through 208 )CL99 - 20887 - 196
1515chain 'C' and (resid 209 through 387 )CL209 - 387197 - 375
1616chain 'C' and (resid 388 through 499 )CL388 - 499376 - 487
1717chain 'C' and (resid 500 through 531 )CL500 - 531488 - 519

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