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- PDB-6nn7: The structure of human liver pyruvate kinase, hLPYK-GGG -

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Basic information

Entry
Database: PDB / ID: 6nn7
TitleThe structure of human liver pyruvate kinase, hLPYK-GGG
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 / Pyruvate metabolism / response to metal ion / monosaccharide binding / Glycolysis ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / response to metal ion / monosaccharide binding / Glycolysis / response to ATP / Regulation of gene expression in beta cells / potassium ion binding / 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 / 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
CITRATE ANION / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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
E: Pyruvate kinase PKLR
D: Pyruvate kinase PKLR
F: Pyruvate kinase PKLR
G: Pyruvate kinase PKLR
H: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,21941
Polymers467,4968
Non-polymers2,72333
Water6,882382
1
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)235,42424
Polymers233,7484
Non-polymers1,67620
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21940 Å2
ΔGint-47 kcal/mol
Surface area69700 Å2
MethodPISA
2
E: Pyruvate kinase PKLR
F: Pyruvate kinase PKLR
G: Pyruvate kinase PKLR
H: Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,79517
Polymers233,7484
Non-polymers1,04713
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19980 Å2
ΔGint-72 kcal/mol
Surface area65550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.365, 106.205, 151.711
Angle α, β, γ (deg.)76.44, 80.06, 71.37
Int Tables number1
Space group name H-MP1

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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: 58437.020 Da / Num. of mol.: 8 / Fragment: UNP residues 34-574 / Mutation: Del529, S531G
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
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 / pH: 6 / Details: 0.2 M ammonium citrate, pH 6.0, 24% 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: May 5, 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: 2.32→39.06 Å / Num. obs: 175876 / % possible obs: 89.4 % / Redundancy: 3.9 % / Net I/σ(I): 12.3
Reflection shellResolution: 2.32→2.36 Å

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Processing

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

4ip7


Resolution: 2.32→39.06 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.07
RfactorNum. reflection% reflection
Rfree0.2514 2000 1.14 %
Rwork0.1913 --
obs0.192 175816 89.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28447 0 178 382 29007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01229023
X-RAY DIFFRACTIONf_angle_d1.25239210
X-RAY DIFFRACTIONf_dihedral_angle_d18.05617728
X-RAY DIFFRACTIONf_chiral_restr0.0634564
X-RAY DIFFRACTIONf_plane_restr0.0085113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.319-2.3770.30461300.248511360X-RAY DIFFRACTION82
2.377-2.44130.29141460.233312699X-RAY DIFFRACTION91
2.4413-2.51310.33161450.225612513X-RAY DIFFRACTION90
2.5131-2.59420.30281430.216712441X-RAY DIFFRACTION89
2.5942-2.68690.28641400.218112110X-RAY DIFFRACTION87
2.6869-2.79440.26381340.211911670X-RAY DIFFRACTION84
2.7944-2.92160.29441480.209312874X-RAY DIFFRACTION93
2.9216-3.07550.28121460.20912727X-RAY DIFFRACTION92
3.0755-3.26810.25641460.208612682X-RAY DIFFRACTION91
3.2681-3.52030.24851400.195712242X-RAY DIFFRACTION88
3.5203-3.87430.27451430.183312428X-RAY DIFFRACTION90
3.8743-4.43430.23421510.159112985X-RAY DIFFRACTION93
4.4343-5.58410.1821400.16312219X-RAY DIFFRACTION88
5.5841-39.06760.23521480.188712866X-RAY DIFFRACTION93

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