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- PDB-6v74: Crystal Structure of Human PKM2 in Complex with L-asparagine -

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Basic information

Entry
Database: PDB / ID: 6v74
TitleCrystal Structure of Human PKM2 in Complex with L-asparagine
ComponentsPyruvate kinase PKM
KeywordsTRANSFERASE / glycolytic enzyme / tetramer / amino acid binding
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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / ASPARAGINE / 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: 2.32 Å
AuthorsNandi, S. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CLP 1506181 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Biochemical and structural insights into how amino acids regulate pyruvate kinase muscle isoform 2.
Authors: Nandi, S. / Dey, M.
History
DepositionDec 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: 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 1.2Sep 30, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)244,05741
Polymers240,2004
Non-polymers3,85737
Water2,810156
1
A: Pyruvate kinase PKM
C: Pyruvate kinase PKM
hetero molecules

D: Pyruvate kinase PKM
hetero molecules

B: Pyruvate kinase PKM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,05741
Polymers240,2004
Non-polymers3,85737
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area25310 Å2
ΔGint-161 kcal/mol
Surface area63390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.990, 154.580, 92.150
Angle α, β, γ (deg.)90.000, 102.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 8 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: 60050.102 Da / Num. of mol.: 4
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
#5: 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.: 4 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 8 types, 189 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaBr, 0.1 M Bis-Tris propane, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.32→77.747 Å / Num. all: 92793 / Num. obs: 92793 / % possible obs: 97.2 % / Redundancy: 6.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Rsym value: 0.057 / Net I/av σ(I): 11.7 / Net I/σ(I): 19.9 / Num. measured all: 632664
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.32-2.455.80.5841.372775125540.2920.7220.5842.490.2
2.45-2.597.20.4391.893708131060.1960.5270.4393.799.7
2.59-2.776.40.292.577704120590.1490.3760.29697.3
2.77-36.70.1594.977535115200.0730.1910.15910.299.9
3-3.287.10.0948.275104105730.0420.1130.09417.899.9
3.28-3.676.70.05812.66091190430.0290.0740.05827.394.1
3.67-4.246.90.03817.95610381370.0180.0470.03838.796.1
4.24-5.197.60.02922.95430471680.0120.0330.02950.499.9
5.19-7.347.50.0321.94191955690.0130.0360.0349.899.9
7.34-77.7477.40.0230.72260130640.0090.0240.0260.898.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALA3.3.22data scaling
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NU1

6nu1


Resolution: 2.32→58.62 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2748 4610 4.97 %
Rwork0.2328 88065 -
obs0.2349 92675 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.2 Å2 / Biso mean: 49.9406 Å2 / Biso min: 25.44 Å2
Refinement stepCycle: final / Resolution: 2.32→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14037 0 233 156 14426
Biso mean--52.54 46.5 -
Num. residues----1955
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 (%)
2.32-2.350.38611430.32882517266084
2.35-2.370.32191500.29612686283688
2.37-2.40.3621510.28242758290992
2.4-2.430.33681560.2782811296794
2.43-2.470.33411390.27282963310297
2.47-2.50.33371590.265429953154100
2.5-2.530.30791720.265930433215100
2.53-2.570.31761620.264229473109100
2.57-2.610.32441460.285130533199100
2.61-2.660.39471410.35122799294094
2.66-2.70.35841640.35062877304194
2.7-2.750.28171510.266729533104100
2.75-2.80.33261700.259230693239100
2.8-2.860.29841750.263530083183100
2.86-2.920.33281520.252629653117100
2.92-2.990.29531500.248330383188100
2.99-3.070.28781560.241130333189100
3.07-3.150.28971290.244930373166100
3.15-3.240.30551560.243130313187100
3.24-3.350.28271500.248430063156100
3.35-3.470.33961550.272679283489
3.47-3.60.28781860.23362975316199
3.6-3.770.26821440.23092801294593
3.77-3.970.2861320.23242730286290
3.97-4.220.23071180.207530973215100
4.22-4.540.23451800.184730023182100
4.54-50.21291420.18630603202100
5-5.720.25771470.220730553202100
5.72-7.20.25451720.226230243196100
7.2-58.620.19841620.18693053321599

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