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

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Basic information

Entry
Database: PDB / ID: 5wsb
TitlePyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate, allosteric activators AMP and Glucose 6-Phosphate
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 / phosphorylation / 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 / 6-O-phosphono-alpha-D-glucopyranose / : / OXALATE ION / PHOSPHATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsZhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research FoundationS916137 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 1.2Jul 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_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.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.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 1.3Nov 8, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)207,16523
Polymers204,0574
Non-polymers3,10819
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16960 Å2
ΔGint-120 kcal/mol
Surface area66460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.631, 125.631, 144.514
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: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / 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
2
1
3
4
5
6

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Components

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Protein / Sugars , 2 types, 8 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
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 425 molecules

#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 3.23 Å3/Da / Density % sol: 61.88 %
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, 5 mM D-glucose 6-phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.264
11-K, -H, -L20.255
11-h,-k,l30.24
11K, H, -L40.242
ReflectionResolution: 2.25→62.82 Å / Num. obs: 120301 / % possible obs: 99.3 % / Redundancy: 5.1 % / Net I/σ(I): 9.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.4 / % possible all: 92.1

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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: 2.25→62.82 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.799 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22782 5944 4.9 %RANDOM
Rwork0.18696 ---
obs0.18898 114312 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.436 Å2
Baniso -1Baniso -2Baniso -3
1-9.05 Å20 Å20 Å2
2--9.05 Å20 Å2
3----18.1 Å2
Refinement stepCycle: 1 / Resolution: 2.25→62.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14172 0 195 410 14777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914564
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214068
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.98819804
X-RAY DIFFRACTIONr_angle_other_deg0.666332420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43151880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52323.243592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.066152448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.80515148
X-RAY DIFFRACTIONr_chiral_restr0.090.22380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022808
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_it2.1172.0697532
X-RAY DIFFRACTIONr_mcbond_other2.1172.0687531
X-RAY DIFFRACTIONr_mcangle_it2.9573.0989408
X-RAY DIFFRACTIONr_mcangle_other2.9573.0989409
X-RAY DIFFRACTIONr_scbond_it2.1952.1777032
X-RAY DIFFRACTIONr_scbond_other2.162.1737004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9253.2210361
X-RAY DIFFRACTIONr_long_range_B_refined4.53239.76461116
X-RAY DIFFRACTIONr_long_range_B_other4.52939.7360885
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)
11A292580.07
12B292580.07
21A289440.08
22C289440.08
31A289460.08
32D289460.08
41B289000.08
42C289000.08
51B288860.09
52D288860.09
61C291560.07
62D291560.07
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.703 370 -
Rwork0.647 7960 -
obs--92.99 %
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)
11.701-0.41680.05491.26330.09790.7875-0.1102-0.01150.15550.11150.1199-0.2932-0.0490.1328-0.00970.17570.0163-0.02870.2769-0.0370.0709-24.1323-2.4131-17.0862
21.41770.4994-0.04452.4581-0.33493.138-0.0314-0.0040.0360.00190.02370.05540.0840.02680.00770.18560.0278-0.00160.2089-0.01890.0944-13.8852-24.9678-39.3461
30.69880.07030.07370.8435-0.17260.9517-0.03510.0166-0.0950.01840.0369-0.04350.0561-0.0434-0.00180.11680.019600.2415-0.02830.0168-32.544-9.5699-28.1681
42.1695-0.14710.36450.0916-0.09661.50880.0089-0.08120.14220.10650.0022-0.0147-0.0327-0.0288-0.0110.14930.0334-0.00830.2496-0.00810.0108-50.56641.3135-13.0078
51.48330.1922-0.27491.59130.0510.9025-0.0743-0.0537-0.2075-0.07670.0673-0.46520.03110.12690.00710.1781-0.03190.03630.2817-0.03610.1537-24.13382.4687-65.5813
61.27990.2492-0.32091.67650.10783.085-0.0531-0.00580.063-0.01380.017-0.0155-0.12350.01890.03610.1991-0.0236-0.01490.2073-0.01160.0572-13.939825.0026-43.4728
70.7160.0661-0.12150.9619-0.26720.9949-0.03790.00460.1007-0.01520.036-0.0843-0.0512-0.05310.00190.1085-0.0125-0.0020.2398-0.02590.0257-32.53569.5635-54.5643
82.22090.0342-0.26010.3687-0.10531.15860.01550.1126-0.1278-0.12930.0148-0.01010.04440.0018-0.03030.1315-0.0412-0.00410.2512-0.00910.01-50.5806-1.2933-69.7228
91.28790.30970.0790.7792-0.42951.3739-0.11970.0867-0.01610.05610.04110.25210.0165-0.29250.07870.17170.0510.04880.3305-0.02240.1531-100.36773.3096-17.0086
101.2264-0.60430.07371.33660.60092.3113-0.0676-0.23190.08660.08340.1391-0.0226-0.0747-0.0403-0.07150.2536-0.0038-0.00030.32630.0570.1989-111.629223.2831-39.7745
110.71330.0648-0.21280.87640.13241.0333-0.055-0.02250.12720.02880.05560.0376-0.1269-0.0556-0.00060.1460.0324-0.01860.2520.0240.0284-92.072310.0315-28.3842
122.2751-0.4237-0.06380.47220.00221.3914-0.0202-0.1465-0.10650.0990.02320.05420.07970.0018-0.0030.13630.01860.00420.25380.00160.0083-73.9709-0.4153-12.9136
130.5458-0.3468-0.05031.773-0.25311.1782-0.0583-0.09550.0138-0.06230.03640.41340.0188-0.23760.02180.1548-0.0558-0.02120.3207-0.00770.1281-100.4039-3.3035-65.6746
140.28470.0109-0.11171.95780.42412.2399-0.06480.2038-0.1158-0.03650.14270.03640.1092-0.0805-0.07780.2646-0.0022-0.0180.33550.04620.211-111.5458-23.3441-42.955
150.7248-0.12390.27460.94560.20821.0153-0.06510.0298-0.1271-0.03730.08020.06340.1278-0.0529-0.01510.1414-0.03330.01470.24310.03270.0307-92.0747-10.0347-54.3238
161.88880.21240.11160.4739-0.02751.0369-0.0170.14060.0834-0.1047-0.00720.047-0.0602-0.01530.02430.1438-0.0217-0.00770.25430.00810.0075-73.91250.3396-69.8508
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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