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- PDB-6nn5: The structure of human liver pyruvate kinase, hLPYK-W527H -

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Basic information

Entry
Database: PDB / ID: 6nn5
TitleThe structure of human liver pyruvate kinase, hLPYK-W527H
ComponentsPyruvate kinase PKLR
KeywordsTRANSFERASE / pyruvate kinase / allosteric / glycolysis
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / monosaccharide binding / response to metal ion / Glycolysis / response to ATP ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / monosaccharide binding / response to metal ion / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to glucose / response to cAMP / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / phosphorylation / magnesium ion binding / extracellular exosome / ATP binding / 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
Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å
AuthorsMcFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Fenton, A.W. / Lamb, A.L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM115340 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM127655 United States
National Science Foundation (NSF, United States)CHE1403293 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)T32GM08545 United States
American Heart AssociationPRE33960374 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Changes in the allosteric site of human liver pyruvate kinase upon activator binding include the breakage of an intersubunit cation-pi bond.
Authors: McFarlane, J.S. / Ronnebaum, T.A. / Meneely, K.M. / Chilton, A. / Fenton, A.W. / Lamb, A.L.
History
DepositionJan 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 PKLR
B: Pyruvate kinase PKLR
C: Pyruvate kinase PKLR
D: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,79026
Polymers234,0644
Non-polymers1,72622
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22250 Å2
ΔGint-43 kcal/mol
Surface area56900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.010, 204.624, 112.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-716-

HOH

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Components

#1: Protein
Pyruvate kinase PKLR / / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 58516.098 Da / Num. of mol.: 4 / Fragment: UNP residues 34-574 / Mutation: W527H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli (E. coli) / References: UniProt: P30613, pyruvate kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Description: Crystals grew as rectangular prisms within two days and reached full size within two weeks.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.325 M ammonium citrate dibasic, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.256→102.312 Å / Num. obs: 84688 / % possible obs: 90.4 % / Redundancy: 6.6 % / Net I/σ(I): 14.9
Reflection shellResolution: 2.256→2.327 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IP7

4ip7


Resolution: 2.256→54.182 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.36
RfactorNum. reflection% reflection
Rfree0.2644 4178 4.94 %
Rwork0.2254 --
obs0.2274 84583 64.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.256→54.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12701 0 112 196 13009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212991
X-RAY DIFFRACTIONf_angle_d1.26817521
X-RAY DIFFRACTIONf_dihedral_angle_d16.4567956
X-RAY DIFFRACTIONf_chiral_restr0.062018
X-RAY DIFFRACTIONf_plane_restr0.0082287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2564-2.2820.3361780.25561469X-RAY DIFFRACTION36
2.282-2.30880.3183650.22781563X-RAY DIFFRACTION38
2.3088-2.3370.3003910.22491605X-RAY DIFFRACTION40
2.337-2.36660.272860.2311604X-RAY DIFFRACTION39
2.3666-2.39770.3327800.22921721X-RAY DIFFRACTION42
2.3977-2.43060.3292940.2411736X-RAY DIFFRACTION43
2.4306-2.46530.32111060.2381808X-RAY DIFFRACTION44
2.4653-2.50210.3343820.25741921X-RAY DIFFRACTION46
2.5021-2.54120.3181130.24991954X-RAY DIFFRACTION48
2.5412-2.58290.29771090.24712026X-RAY DIFFRACTION50
2.5829-2.62740.2941120.2542187X-RAY DIFFRACTION53
2.6274-2.67520.3176310.2486677X-RAY DIFFRACTION53
2.6752-2.72660.30681200.24851784X-RAY DIFFRACTION58
2.7266-2.78230.33771350.24692528X-RAY DIFFRACTION62
2.7823-2.84280.30641350.23762664X-RAY DIFFRACTION64
2.8428-2.90890.28321530.23262716X-RAY DIFFRACTION67
2.9089-2.98160.271510.2422889X-RAY DIFFRACTION70
2.9816-3.06220.29351820.24062987X-RAY DIFFRACTION73
3.0622-3.15230.24511470.24763187X-RAY DIFFRACTION77
3.1523-3.25410.26851510.24553357X-RAY DIFFRACTION81
3.2541-3.37040.2731860.22543527X-RAY DIFFRACTION86
3.3704-3.50530.2841250.23362518X-RAY DIFFRACTION61
3.5053-3.66480.2361720.21593606X-RAY DIFFRACTION98
3.6648-3.85790.26982120.20463776X-RAY DIFFRACTION98
3.8579-4.09960.25041820.20243442X-RAY DIFFRACTION83
4.0996-4.4160.21952020.18914173X-RAY DIFFRACTION100
4.416-4.86010.21182160.18234170X-RAY DIFFRACTION99
4.8601-5.56280.24082000.21184215X-RAY DIFFRACTION100
5.5628-7.00610.28292320.25664243X-RAY DIFFRACTION100
7.0061-54.1980.26342300.25984352X-RAY DIFFRACTION98

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