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- PDB-4wj8: Human Pyruvate Kinase M2 Mutant C424A -

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Basic information

Entry
Database: PDB / ID: 4wj8
TitleHuman Pyruvate Kinase M2 Mutant C424A
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / Glycolysis / Allostery
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
1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALIC ACID / PHOSPHATE ION / Pyruvate kinase PKM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsMitchell, T. / Yuan, M. / McNae, I. / Morgan, H. / Walkinshaw, M.D.
CitationJournal: To Be Published
Title: Human Pyruvate Kinase M2 Mutant C424A
Authors: Mitchell, T. / Yuan, M. / McNae, I. / Morgan, H. / Walkinshaw, M.D.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: Pyruvate kinase PKM
D: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,85628
Polymers240,6254
Non-polymers2,23124
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23760 Å2
ΔGint-204 kcal/mol
Surface area70930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.359, 115.260, 109.401
Angle α, β, γ (deg.)90.00, 114.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVALAA15 - 53035 - 550
21THRTHRVALVALBB15 - 53035 - 550
12GLNGLNVALVALAA16 - 53036 - 550
22GLNGLNVALVALCC16 - 53036 - 550
13THRTHRVALVALAA15 - 53035 - 550
23THRTHRVALVALDD15 - 53035 - 550
14GLNGLNVALVALBB16 - 53036 - 550
24GLNGLNVALVALCC16 - 53036 - 550
15THRTHRPROPROBB15 - 53135 - 551
25THRTHRPROPRODD15 - 53135 - 551
16GLNGLNVALVALCC16 - 53036 - 550
26GLNGLNVALVALDD16 - 53036 - 550

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Sugars , 2 types, 6 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: 60156.188 Da / Num. of mol.: 4 / Mutation: C424A
Source method: isolated from a genetically manipulated source
Details: Human Pyruvate Kinase M2 Mutant C424A / Source: (gene. exp.) Homo sapiens (human) / Gene: PKM, OIP3, PK2, PK3, PKM2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14618, pyruvate kinase
#3: 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


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 7 types, 185 molecules

#2: Chemical
ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H2O4
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium cacodylate, Triethanolamine, MgCl2, KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.87→49.88 Å / Num. all: 153526 / Num. obs: 43988 / % possible obs: 90.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SRD

3srd


Resolution: 2.87→49.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 21.169 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24318 2212 5 %RANDOM
Rwork0.20023 ---
obs0.2024 41736 90.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.939 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.87→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15822 0 127 163 16112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01916183
X-RAY DIFFRACTIONr_bond_other_d0.0030.0215978
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.97721865
X-RAY DIFFRACTIONr_angle_other_deg0.826336796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50752064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22123.925665
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.252152909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.04415124
X-RAY DIFFRACTIONr_chiral_restr0.0560.22518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023430
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4967.0658268
X-RAY DIFFRACTIONr_mcbond_other2.4957.0658267
X-RAY DIFFRACTIONr_mcangle_it4.17810.59410328
X-RAY DIFFRACTIONr_mcangle_other4.17810.59410329
X-RAY DIFFRACTIONr_scbond_it2.6157.4317915
X-RAY DIFFRACTIONr_scbond_other2.6157.4317915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.49411.03311538
X-RAY DIFFRACTIONr_long_range_B_refined7.96655.37217811
X-RAY DIFFRACTIONr_long_range_B_other7.96655.37417811
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A322440.06
12B322440.06
21A323470.06
22C323470.06
31A322400.06
32D322400.06
41B325770.05
42C325770.05
51B325800.06
52D325800.06
61C323580.05
62D323580.05
LS refinement shellResolution: 2.873→2.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 173 -
Rwork0.354 3134 -
obs--92.19 %

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