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

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Basic information

Entry
Database: PDB / ID: 4hyv
TitlePyruvate kinase (PYK) from Trypanosoma brucei in the presence of Magnesium, PEP 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 / kinase activity / magnesium ion binding / ATP binding
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 / : / PHOSPHOENOLPYRUVATE / Pyruvate kinase 1
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
A: Pyruvate kinase 1
B: Pyruvate kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,35012
Polymers109,0792
Non-polymers1,27110
Water15,439857
1
A: Pyruvate kinase 1
B: Pyruvate kinase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)220,70024
Polymers218,1584
Non-polymers2,54120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area20770 Å2
ΔGint-160 kcal/mol
Surface area71430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.410, 108.930, 263.340
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-1005-

CL

21B-1359-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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
#5: 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 , 6 types, 865 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
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 3.4 Å3/Da / Density % sol: 63.82 %
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: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→65.83 Å / Num. obs: 66318 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.42 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: 2.3→65.17 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.984 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.188 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18839 3366 5.1 %RANDOM
Rwork0.1462 ---
obs0.14836 62951 99.98 %-
all-66318 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2---0.24 Å2-0 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 71 857 8524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.027856
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.97410652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37851024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37924.347329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.359151418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0861556
X-RAY DIFFRACTIONr_chiral_restr0.1230.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215808
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 216 -
Rwork0.218 4354 -
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)
15.3507-3.33563.75262.4753-3.20854.5628-0.0784-0.076-0.1366-0.09450.0970.03990.2145-0.1748-0.01850.1571-0.01430.0280.10480.00760.0612-57.352-40.169425.5116
20.56120.3686-0.28120.5810.20870.6037-0.04030.0670.1852-0.0080.07440.18420.0202-0.0136-0.03410.08350.07550.01610.11060.01660.1408-86.0969-27.209341.5496
30.5917-1-1.7964.88723.50395.52890.3829-0.07170.1455-1.11480.0165-0.1178-1.20790.1734-0.39940.3946-0.03880.12240.0993-0.07350.0941-67.99-8.162962.8569
40.31370.1283-0.08780.35080.00730.05190.0113-0.03710.11330.0567-0.00590.04550.01780.007-0.00540.13980.02670.03640.1162-0.01270.0756-73.3203-30.230848.5275
50.642-0.1568-0.10170.64620.11840.0340.0180.0574-0.02630.0061-0.02090.0694-0.0169-0.01540.00280.08310.0070.02330.14460.02850.0857-81.2005-52.372838.2297
64.49565.28262.85968.04765.22233.70750.0775-0.315-0.3074-0.14730.0135-0.247-0.21290.176-0.0910.13790.00770.02910.15450.05360.0792-55.9927-39.581650.3682
71.0925-0.092-0.38530.0464-0.03480.26020.0022-0.08540.3772-0.02610.0303-0.09790.0716-0.0159-0.03240.1115-0.0505-0.01640.0319-0.0410.2832-41.6171-11.661634.2243
82.5061-1.0608-0.21892.04080.89550.6859-0.0539-0.1895-0.1361-0.1873-0.01340.0494-0.1629-0.04440.06730.11090.03190.00280.11380.07570.0704-68.4186-12.54588.6436
90.36750.0467-0.01140.2132-0.12860.1496-0.05510.07850.16910.01840.0116-0.02850.0751-0.00910.04350.1293-0.00140.00290.09010.04680.1169-49.6298-22.144427.2153
100.7242-0.30010.05230.9375-0.13310.0195-0.03820.0010.13930.07020.0172-0.114-0.0051-0.0060.0210.0862-0.0165-0.01560.1104-0.00450.1205-29.7167-34.411437.6108
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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