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- PDB-4ip7: Structure of the S12D variant of human liver pyruvate kinase in c... -

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Basic information

Entry
Database: PDB / ID: 4ip7
TitleStructure of the S12D variant of human liver pyruvate kinase in complex with citrate and FBP.
ComponentsPyruvate kinase isozymes L
KeywordsTRANSFERASE / kinase / glycolysis / allosteric / phosphorylation mimic / liver
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 / response to metal ion / monosaccharide binding / 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 / response to metal ion / monosaccharide binding / 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 / 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
ADENOSINE / 1,6-di-O-phosphono-beta-D-fructofuranose / CITRATE ANION / : / DI(HYDROXYETHYL)ETHER / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHolyoak, T. / Fenton, A.W.
CitationJournal: Biochemistry / Year: 2013
Title: Energetic Coupling between an Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase.
Authors: Holyoak, T. / Zhang, B. / Deng, J. / Tang, Q. / Prasannan, C.B. / Fenton, A.W.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: 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
Item: _chem_comp.pdbx_synonyms / _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 isozymes L
B: Pyruvate kinase isozymes L
C: Pyruvate kinase isozymes L
D: Pyruvate kinase isozymes L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,31234
Polymers234,3694
Non-polymers3,94330
Water23,8521324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25420 Å2
ΔGint-130 kcal/mol
Surface area71520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.140, 205.078, 83.910
Angle α, β, γ (deg.)90.000, 92.150, 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 isozymes L / Pyruvate kinase 1 / L-type pyruvate kinase / liver pyruvate kinase


Mass: 58592.176 Da / Num. of mol.: 4 / Fragment: liver isozyme / Mutation: S12D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PK1, PKL, PKLR / Production host: Escherichia coli (E. coli) / Strain (production host): FF50 / References: UniProt: P30613, pyruvate kinase
#4: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 8 types, 1350 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1324 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 50 mM sodium citrate (pH 4.9), 26 mM MnCl2, 3-5% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2008
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 237180 / % possible obs: 97.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.069 / Χ2: 1.029 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.70.698226280.948193.3
1.86-1.944.10.657239881.127199.2
1.94-2.034.30.383239681.046199.3
2.03-2.134.30.26239781.08198.9
2.13-2.274.20.228237941.024198.1
2.27-2.444.30.13235950.994197.3
2.44-2.694.30.097232861.041196
2.69-3.084.30.072235430.986197.1
3.08-3.884.50.058241381.068199.3
3.88-504.90.036242620.974199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VGB

2vgb


Resolution: 1.8→37.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2365 / WRfactor Rwork: 0.1949 / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8214 / SU B: 5.671 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1145 / SU Rfree: 0.1153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 11896 5 %RANDOM
Rwork0.1873 ---
obs0.1892 236781 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.31 Å2 / Biso mean: 41.9854 Å2 / Biso min: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15291 0 226 1324 16841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01916097
X-RAY DIFFRACTIONr_angle_refined_deg2.221.98321874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41552103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3423.015680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.167152748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78315163
X-RAY DIFFRACTIONr_chiral_restr0.1710.22543
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112045
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 778 -
Rwork0.332 15133 -
all-15911 -
obs--89.42 %
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)
11.0562-1.4138-0.22964.96992.10352.1191-0.0804-0.009-0.17680.2705-0.12610.36370.1791-0.25130.20650.0339-0.01160.04990.0762-0.01060.081144.232-32.7115.716
219.2239-2.1238-7.27593.92162.2626.6628-0.3719-1.70230.08330.09020.4084-0.02620.34270.9976-0.03650.0470.09810.05590.5322-0.00330.143980.083-24.16618.496
31.14060.44820.12762.20531.23992.5886-0.11910.1149-0.0724-0.15630.0443-0.0772-0.11920.14020.07480.0258-0.01230.01810.0676-0.00390.030352.438-24.4199.636
45.1931-2.46851.87652.2396-0.53733.1073-0.0563-0.0898-0.248-0.13520.08260.20690.0859-0.1308-0.02630.0444-0.02030.00910.0893-0.02970.062330.422-30.959-0.777
54.9992.47551.57362.10480.6281.4372-0.07370.3255-0.101-0.1480.1524-0.2176-0.0095-0.0622-0.07870.0663-0.0250.01960.11290.01630.04128.2352.935-21.322
611.4445-0.0401-1.638311.63920.69753.12020.1205-0.68271.80890.443-0.09450.9931-0.3849-0.5944-0.0260.24680.14080.08870.641-0.1430.6665-10.66327.762-5.317
71.77091.26490.20822.07730.24571.53510.1538-0.1587-0.09470.1369-0.0281-0.04020.0661-0.242-0.12570.0349-0.0197-0.00140.10730.03370.02036.6955.409-9.917
84.4161-1.80761.55373.2552-1.97251.79680.04230.256-0.1153-0.3068-0.06320.00760.10920.0980.02090.0528-0.02920.01540.10250.00720.073816.115-17.673-14.069
90.9320.31891.19241.43862.4176.0252-0.1658-0.03250.1164-0.21850.1579-0.1618-0.49190.31910.00790.0581-0.0045-0.00010.1389-0.01850.063457.802-0.47631.616
109.1945-1.2233-5.14868.04550.864814.6168-1.1031-1.28-0.86510.85870.09580.19112.05640.90821.00720.72120.22510.34290.61320.19940.191240.901-27.83350.07
111.39550.17780.14142.26421.48542.0628-0.202-0.26490.1024-0.001-0.08860.213-0.2467-0.1960.29060.08420.0739-0.04610.1433-0.04550.045945.476-5.26533.227
121.3725-1.31910.81653.1868-1.18384.7139-0.00350.05490.2031-0.00640.0347-0.1855-0.13610.298-0.03120.16570.0337-0.02980.1193-0.05040.061850.21217.94924.602
131.49872.1292-0.28335.8387-1.6361.08170.2027-0.27730.18750.4352-0.16870.2037-0.139-0.0279-0.0340.087-0.01450.04610.1057-0.02540.076822.87132.702-4.15
1414.90778.08384.86555.86341.44637.5945-1.18034.0047-0.2553-0.92111.5908-0.17-0.53480.356-0.41050.5052-0.17240.21451.6973-0.00440.107825.01224.278-42.496
151.9481.01560.09972.40620.3110.82910.03440.0726-0.1076-0.15960.0512-0.3624-0.07140.0815-0.08560.0652-0.01620.05530.0645-0.01230.073130.32125.115-14.559
162.3234-0.06911.30233.0196-2.52974.5931-0.0526-0.18870.14590.37480.1-0.0874-0.257-0.1162-0.04750.1109-0.0222-0.01590.1159-0.00580.092538.26931.1369.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 130
2X-RAY DIFFRACTION2A131 - 228
3X-RAY DIFFRACTION3A232 - 411
4X-RAY DIFFRACTION4A412 - 543
5X-RAY DIFFRACTION5B25 - 146
6X-RAY DIFFRACTION6B147 - 234
7X-RAY DIFFRACTION7B235 - 411
8X-RAY DIFFRACTION8B412 - 543
9X-RAY DIFFRACTION9C26 - 128
10X-RAY DIFFRACTION10C129 - 234
11X-RAY DIFFRACTION11C235 - 411
12X-RAY DIFFRACTION12C412 - 543
13X-RAY DIFFRACTION13D21 - 125
14X-RAY DIFFRACTION14D126 - 219
15X-RAY DIFFRACTION15D220 - 411
16X-RAY DIFFRACTION16D412 - 543

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