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- PDB-4hyw: Pyruvate kinase (PYK) from Trypanosoma brucei in the presence of ... -

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Basic information

Entry
Database: PDB / ID: 4hyw
TitlePyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium and F26BP
ComponentsPyruvate kinase 1
KeywordsTRANSFERASE / Allosteric regulation / tetramer / Pyruvate Kinase / FRUCTOSE-2 / 6-DIPHOSPHATE binding / Phosphoenolpyruvate binding / cytosol
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / 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
2,6-di-O-phosphono-beta-D-fructofuranose / : / Pyruvate kinase 1
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhong, W. / Morgan, H.P. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: `In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase.
Authors: Zhong, W. / Morgan, H.P. / McNae, I.W. / Michels, P.A. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: 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 / pdbx_struct_conn_angle / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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
B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,01410
Polymers109,0792
Non-polymers9358
Water10,539585
1
B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules

B: Pyruvate kinase 1
A: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,02720
Polymers218,1584
Non-polymers1,86916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area18780 Å2
ΔGint-132 kcal/mol
Surface area72890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.680, 109.000, 268.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-504-

CL

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Pyruvate kinase 1 / PK 1


Mass: 54539.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PYK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30615, pyruvate kinase
#4: Sugar ChemComp-FDP / 2,6-di-O-phosphono-beta-D-fructofuranose / FRUCTOSE-2,6-DIPHOSPHATE / 2,6-di-O-phosphono-beta-D-fructose / 2,6-di-O-phosphono-D-fructose / 2,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf2PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 591 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 3.48 Å3/Da / Density % sol: 64.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 6-20% PEG 8,000, 10-20% glycerol, 50 mM TEA buffer, 100 mM KCl, 50 mM MgCl2, 80 uM F26BP, 800 uM Ponceau S., pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.35→134.19 Å / Num. obs: 63644 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.35→2.48 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→54.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.308 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.216 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19873 3227 5.1 %RANDOM
Rwork0.16385 ---
obs0.16566 60417 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.851 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å2-0 Å20 Å2
2---0.53 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→54.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7579 0 51 585 8215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027823
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.97110605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34651019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32924.32331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.181557
X-RAY DIFFRACTIONr_chiral_restr0.0820.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215793
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 227 -
Rwork0.258 4205 -
obs--100 %
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)
110.6268-6.841975.0678-5.73636.89550.20950.0224-0.2846-0.24130.01880.1940.3071-0.0442-0.22830.3010.01250.0120.27810.05420.3124-57.4798-40.248825.7589
20.51770.42-0.24910.4347-0.21750.1257-0.05850.03310.2128-0.00130.15570.23980.0211-0.0267-0.09720.23190.16050.03860.32990.03110.4145-86.3111-27.297441.6713
34.01490.0393-2.01014.7439-3.21253.2278-0.7685-0.6570.73140.24130.9647-0.41220.0175-0.2472-0.19620.6738-0.00210.0060.5622-0.42860.3691-65.7494-11.498267.5548
40.82780.0182-0.18820.15150.06660.09120.0143-0.17630.1462-0.0107-0.03760.0327-0.0127-0.02460.02330.30560.0680.05240.3543-0.01510.2968-73.4789-30.461148.7286
50.9131-0.11-0.06971.160.140.02730.04320.0264-0.0015-0.0051-0.04760.0781-0.0153-0.05680.00450.20830.02930.02630.38220.0510.3139-81.4181-52.431338.2827
61.85233.41132.1979.47036.67614.79980.1105-0.2486-0.2322-0.00950.0675-0.2218-0.09560.1168-0.1780.31410.00820.06480.34050.03110.2971-56.2048-39.728350.5842
71.28660.0875-0.23510.0113-0.01770.04770.0657-0.1190.4088-0.01210.0011-0.0130.02980.0207-0.06680.3741-0.05650.02750.1013-0.00190.5211-41.7872-11.711134.7115
82.2069-1.28240.0361.49220.99571.40830.024-0.1436-0.1662-0.1874-0.0170.0242-0.2453-0.0728-0.0070.34840.0203-0.00170.24260.28890.3487-68.2745-12.57428.6334
90.43560.2022-0.04360.2038-0.02030.3632-0.04160.11370.19210.03910.0613-0.0223-0.0007-0.008-0.01970.3219-0.00090.03270.2520.0520.3682-49.7788-22.136527.5502
100.8016-0.19230.0961.1579-0.2250.0585-0.0103-00.15420.08580.0227-0.1074-0.00640.0367-0.01240.2419-0.0309-0.00890.3211-0.04730.3608-29.848-34.411437.8432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 14
2X-RAY DIFFRACTION2A15 - 87
3X-RAY DIFFRACTION3A88 - 189
4X-RAY DIFFRACTION4A190 - 357
5X-RAY DIFFRACTION5A358 - 499
6X-RAY DIFFRACTION6B2 - 14
7X-RAY DIFFRACTION7B15 - 87
8X-RAY DIFFRACTION8B88 - 189
9X-RAY DIFFRACTION9B190 - 357
10X-RAY DIFFRACTION10B358 - 499

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