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- PDB-5ws9: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex ... -

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Basic information

Entry
Database: PDB / ID: 5ws9
TitlePyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, ATP and allosteric activator AMP
ComponentsPyruvate kinase
KeywordsTRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery / synergism / phospho transferase
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / : / OXALATE ION / PHOSPHATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation funding through SMARTS916137 Singapore
Singapore-MIT Alliance for Research and Technology (SMART) FellowshipS900184 Singapore
CitationJournal: Nat Commun / Year: 2017
Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.
Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C.
History
DepositionDec 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,47029
Polymers204,0574
Non-polymers4,41325
Water25,9421440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-155 kcal/mol
Surface area66090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.190, 127.190, 144.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyruvate kinase / PK


Mass: 51014.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Plasmid: pYUB28b-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase

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Non-polymers , 7 types, 1465 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1440 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 13% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP, 5 mM AMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.9→60.54 Å / Num. obs: 206700 / % possible obs: 100 % / Redundancy: 4.8 % / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WRP

5wrp


Resolution: 1.9→60.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.347 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22292 10685 5.2 %RANDOM
Rwork0.19676 ---
obs0.19812 195933 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----2.43 Å2
Refinement stepCycle: 1 / Resolution: 1.9→60.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14172 0 269 1440 15881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214118
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.99419993
X-RAY DIFFRACTIONr_angle_other_deg0.691332527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26823.227595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.543152458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.815149
X-RAY DIFFRACTIONr_chiral_restr0.0880.22380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022845
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7041.8437552
X-RAY DIFFRACTIONr_mcbond_other1.7021.8437551
X-RAY DIFFRACTIONr_mcangle_it2.3592.7539440
X-RAY DIFFRACTIONr_mcangle_other2.362.7549441
X-RAY DIFFRACTIONr_scbond_it3.1112.2437132
X-RAY DIFFRACTIONr_scbond_other2.6092.2357117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7563.24810530
X-RAY DIFFRACTIONr_long_range_B_refined6.1537.98863820
X-RAY DIFFRACTIONr_long_range_B_other6.1537.98863821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A295100.08
12B295100.08
21A289120.1
22C289120.1
31A289240.1
32D289240.1
41B287940.1
42C287940.1
51B289120.1
52D289120.1
61C291020.1
62D291020.1
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 820 -
Rwork0.328 14533 -
obs--99.99 %
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)
12.0551-0.6314-0.4911.01930.33232.217-0.09410.22360.4324-0.1044-0.0164-0.047-0.2297-0.07480.11050.15170.0772-0.03620.1190.06620.121773.79687.6821-18.0595
21.2650.6836-0.09682.37940.14895.56250.01880.0792-0.00710.1015-0.0357-0.08030.0273-0.20480.01690.10030.01430.01720.13740.01490.138448.728185.6324.1887
31.29640.09030.41960.99410.25621.99020.03080.0879-0.04930.0145-0.08440.11910.1789-0.06790.05350.12450.06550.02060.0645-0.00550.020571.738776.9239-6.9309
42.702-1.71460.73862.9686-0.03452.38610.13260.2490.0726-0.178-0.1362-0.10960.0670.13270.00350.15740.14160.01280.13980.01140.004490.238266.4151-22.0726
51.2790.5011-0.01372.6738-0.51682.27170.0414-0.11420.16960.1362-0.0910.3548-0.1826-0.1730.04960.170.05640.03020.0585-0.02670.064577.943490.077530.4167
62.7699-0.01180.3061.27510.02845.86660.07840.0908-0.10.1103-0.06280.0447-0.17080.1237-0.01570.1356-0.01170.02320.09410.00380.12692.2331110.76348.1795
71.19730.16180.35641.21090.27631.9761-0.01170.05270.07830.1098-0.0265-0.10010.02730.19240.03820.13250.05620.00670.050.01870.018788.265286.464219.3268
81.285-0.87390.29593.770.41242.3517-0.0321-0.0866-0.06330.29680.04010.09340.1208-0.0101-0.0080.24430.07180.01270.03920.00460.018688.133765.176134.4448
91.9064-0.34840.5791.4576-0.15413.24310.0340.1586-0.3745-0.0376-0.0336-0.05920.53910.334-0.00040.2230.157-0.00220.1621-0.03380.0914117.128623.8637-18.0963
102.8841.0621-0.62242.2376-1.34825.34830.16840.49570.1507-0.2170.00020.0359-0.1286-0.1035-0.16860.27520.0944-0.05250.2699-0.06870.2082140.252824.00164.631
111.2757-0.0395-0.09511.2431-0.32782.70060.10090.10420.10150.0072-0.1173-0.1883-0.03790.37250.01640.11090.083-0.01730.1398-0.00030.0426118.867234.3744-6.709
122.7353-1.717-0.52.9361-0.0392.23850.12970.1719-0.059-0.2115-0.1240.0803-0.0741-0.134-0.00570.16730.1285-0.00880.1214-0.01370.0059100.74345.1414-22.1899
130.89040.28060.09582.78460.66033.52060.0117-0.0098-0.20510.2163-0.0341-0.31830.57810.24690.02240.28980.099-0.02920.06960.0090.0774111.536620.637330.4896
142.97550.6972-1.47441.8451-0.04015.44380.1742-0.24340.08890.4772-0.00160.1439-0.2234-0.0526-0.17260.35690.0451-0.07580.2114-0.01770.20299.88030.6927.7208
151.21830.0353-0.35771.31240.00692.5719-0.00940.0534-0.08550.16420.00460.16980.3231-0.21330.00480.2080.0258-0.01190.0487-0.01260.0355101.572624.379719.1155
161.418-0.7474-0.51013.9175-0.53252.3725-0.0407-0.10940.03680.2520.0592-0.0471-0.1509-0.0001-0.01850.23020.0786-0.01890.04360.00320.0223101.290245.4534.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 70
2X-RAY DIFFRACTION2A71 - 167
3X-RAY DIFFRACTION3A168 - 344
4X-RAY DIFFRACTION4A345 - 467
5X-RAY DIFFRACTION5B2 - 70
6X-RAY DIFFRACTION6B71 - 167
7X-RAY DIFFRACTION7B168 - 344
8X-RAY DIFFRACTION8B345 - 467
9X-RAY DIFFRACTION9C2 - 70
10X-RAY DIFFRACTION10C71 - 167
11X-RAY DIFFRACTION11C168 - 344
12X-RAY DIFFRACTION12C345 - 467
13X-RAY DIFFRACTION13D2 - 70
14X-RAY DIFFRACTION14D71 - 167
15X-RAY DIFFRACTION15D168 - 344
16X-RAY DIFFRACTION16D345 - 467

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