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- PDB-8hgf: Human PKM2 mutant - C326S -

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Basic information

Entry
Database: PDB / ID: 8hgf
TitleHuman PKM2 mutant - C326S
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / mutation / S-sulfhydration / ONCOPROTEIN
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 / protein tyrosine kinase activity / collagen-containing extracellular matrix / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsChen, Y.-C. / Lin, K.-T. / Cheng, H.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan)111-2311-B-007 -009 - Taiwan
CitationJournal: To Be Published
Title: Human PKM2 mutant - C326S
Authors: Chen, Y.-C. / Lin, K.-T. / Cheng, H.-C.
History
DepositionNov 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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
D: Pyruvate kinase PKM
C: Pyruvate kinase PKM


Theoretical massNumber of molelcules
Total (without water)240,7654
Polymers240,7654
Non-polymers00
Water0
1
A: Pyruvate kinase PKM
D: Pyruvate kinase PKM

A: Pyruvate kinase PKM
D: Pyruvate kinase PKM


Theoretical massNumber of molelcules
Total (without water)240,7654
Polymers240,7654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area14380 Å2
ΔGint-79 kcal/mol
Surface area73920 Å2
MethodPISA
2
B: Pyruvate kinase PKM
C: Pyruvate kinase PKM

B: Pyruvate kinase PKM
C: Pyruvate kinase PKM


Theoretical massNumber of molelcules
Total (without water)240,7654
Polymers240,7654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area14040 Å2
ΔGint-83 kcal/mol
Surface area68450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.514, 156.373, 121.586
Angle α, β, γ (deg.)90.00, 114.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 60191.234 Da / Num. of mol.: 4 / Mutation: C326S
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

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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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.4 M ammonium phosphate monobasic, 23% polyethylene glycerol 3350, Tris pH 7.0
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.1→29.79 Å / Num. obs: 55273 / % possible obs: 98.4 % / Redundancy: 3.6 % / Rrim(I) all: 0.068 / Net I/σ(I): 20
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 5394 / Rrim(I) all: 0.601

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QG6

4qg6


Resolution: 3.1→29.79 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 2827 4 %
Rwork0.182 --
obs0.1842 49956 63.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14857 0 0 0 14857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02215101
X-RAY DIFFRACTIONf_angle_d1.85720401
X-RAY DIFFRACTIONf_dihedral_angle_d7.8242094
X-RAY DIFFRACTIONf_chiral_restr0.0732347
X-RAY DIFFRACTIONf_plane_restr0.0172654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.150.3605640.31061551X-RAY DIFFRACTION29
3.15-3.210.3449690.27791648X-RAY DIFFRACTION31
3.21-3.270.3717750.27261813X-RAY DIFFRACTION34
3.27-3.340.2841820.2841964X-RAY DIFFRACTION37
3.34-3.410.3623870.28342116X-RAY DIFFRACTION40
3.41-3.490.3192960.26582269X-RAY DIFFRACTION43
3.49-3.580.32821020.23552503X-RAY DIFFRACTION47
3.58-3.670.30731140.22292754X-RAY DIFFRACTION52
3.67-3.780.26451190.20752956X-RAY DIFFRACTION56
3.78-3.90.23831330.20563167X-RAY DIFFRACTION59
3.9-4.040.22831390.18973382X-RAY DIFFRACTION64
4.04-4.210.25991590.17363697X-RAY DIFFRACTION70
4.21-4.40.2211700.16293963X-RAY DIFFRACTION75
4.4-4.630.20871810.13924341X-RAY DIFFRACTION81
4.63-4.920.18231960.14054534X-RAY DIFFRACTION86
4.92-5.290.21241960.15744769X-RAY DIFFRACTION90
5.29-5.820.21222140.17325198X-RAY DIFFRACTION98
5.82-6.660.26222140.1975198X-RAY DIFFRACTION98
6.66-8.350.22092150.1635162X-RAY DIFFRACTION97
8.36-29.790.2052020.16244828X-RAY DIFFRACTION91
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)
13.3742-0.236-0.47461.406-0.03893.0803-0.0621-0.2997-0.26890.38620.055-0.03440.02210.3367-0.09410.3631-0.131-0.02480.24710.04860.292-9.39461.341193.2084
26.03750.1331-0.70692.64932.19675.5874-0.1291-0.61770.31430.1126-0.52750.8975-0.5479-1.5510.5740.80610.05320.00860.9719-0.20260.7171-30.884623.3985106.3934
34.01810.05911.182.78831.56335.37620.084-0.37610.19920.1254-0.02290.5593-0.6819-0.14430.25680.5097-0.1406-0.00890.2499-0.05010.3978-16.583212.508187.631
44.3377-0.114-0.5782.28620.0425.9640.0617-0.0683-0.3554-0.2418-0.03180.14560.1490.4783-0.02790.3165-0.0603-0.05630.1986-0.06680.3759-1.7339-2.793472.8275
50.88530.9013-1.2051.253-0.48012.3942-0.16470.0885-0.0911-0.2670.21740.12130.2-0.2013-0.13280.4467-0.0876-0.1290.7138-0.09680.605339.47369.506123.8126
61.5448-0.035-0.44031.2979-1.68083.4387-0.21590.0542-0.0136-0.2440.1393-0.1393-0.1704-0.1478-0.02240.5219-0.191-0.07020.2832-0.09480.563350.468931.15177.6905
73.667-0.69071.01513.2931-1.05882.361-0.00220.42150.0921-0.5816-0.2539-0.2955-0.20660.14940.18710.3342-0.04630.07160.63650.05290.461350.203615.691826.4598
83.83541.16590.25935.9672-2.33244.1775-0.192-0.53810.31150.6825-0.035-0.7788-0.18350.17860.14510.3581-0.03180.05930.7822-0.08280.534838.67877.806349.1362
92.8806-0.22191.31062.15440.08752.5105-0.1403-0.10610.4925-0.19310.3466-0.1815-0.50180.77-0.25530.3671-0.06290.02210.2971-0.02570.29841.0709-1.12926.6978
101.46340.83080.3621.38482.78775.2105-0.1910.2153-0.0475-0.28680.22410.16630.17810.04590.02740.5063-0.0114-0.01650.14860.06320.5241-10.6241-18.791318.0882
113.92051.1740.81772.87761.30056.13070.0651-0.2561-0.0180.49150.07110.2689-0.05960.2168-0.16020.35980.0174-0.03420.2527-0.09080.43221.4127-1.659746.2293
123.39320.6488-1.42861.6180.1091.84720.31940.12990.72530.2354-0.15690.0942-0.3077-0.6363-0.10210.51210.03760.00540.8362-0.1080.48955.23413.474687.1554
133.345-0.1383-0.96232.90350.01162.9426-0.1777-0.6211-0.42370.35110.0071-0.32330.65250.05460.13410.5754-0.08840.02310.7179-0.01520.42154.0937-4.853691.1014
143.5747-0.59840.17092.0214-0.05884.27140.0402-0.0280.2261-0.13490.05940.01330.00260.0403-0.0530.2571-0.1370.02730.6411-0.06840.382143.16758.371873.5733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 371 )
4X-RAY DIFFRACTION4chain 'A' and (resid 372 through 531 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 128 )
6X-RAY DIFFRACTION6chain 'B' and (resid 129 through 247 )
7X-RAY DIFFRACTION7chain 'B' and (resid 248 through 388 )
8X-RAY DIFFRACTION8chain 'B' and (resid 389 through 531 )
9X-RAY DIFFRACTION9chain 'D' and (resid 24 through 108 )
10X-RAY DIFFRACTION10chain 'D' and (resid 109 through 371 )
11X-RAY DIFFRACTION11chain 'D' and (resid 372 through 531 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 67 )
13X-RAY DIFFRACTION13chain 'C' and (resid 68 through 370 )
14X-RAY DIFFRACTION14chain 'C' and (resid 371 through 531 )

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