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- PDB-6i2p: Crystal structure of the Mycobacterium tuberculosis PknB kinase d... -

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Basic information

Entry
Database: PDB / ID: 6i2p
TitleCrystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in complex with its substrate GarA
Components
  • Glycogen accumulation regulator GarA
  • Serine/threonine-protein kinase PknB
  • UNK-UNK-UNK-UNK-UNK
KeywordsSIGNALING PROTEIN / kinase / FHA-domain protein
Function / homology
Function and homology information


negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / regulation of cellular respiration / negative regulation of glycolytic process / molecular function inhibitor activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape ...negative regulation of growth rate / negative regulation of fatty acid biosynthetic process / acetyltransferase activator activity / response to host immune response / regulation of cellular respiration / negative regulation of glycolytic process / molecular function inhibitor activity / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / manganese ion binding / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / regulation of DNA-templated transcription / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / : / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Serine/threonine-protein kinase PknB / Glycogen accumulation regulator GarA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsAndre-Leroux, G. / Hindie, V. / Barilone, N. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Sci.Signal. / Year: 2019
Title: Structural insights into the functional versatility of an FHA domain protein in mycobacterial signaling.
Authors: Wagner, T. / Andre-Leroux, G. / Hindie, V. / Barilone, N. / Lisa, M.N. / Hoos, S. / Raynal, B. / Vulliez-Le Normand, B. / O'Hare, H.M. / Bellinzoni, M. / Alzari, P.M.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PknB
B: Serine/threonine-protein kinase PknB
D: Glycogen accumulation regulator GarA
E: Glycogen accumulation regulator GarA
C: UNK-UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47712
Polymers96,1305
Non-polymers1,3477
Water4,107228
1
A: Serine/threonine-protein kinase PknB
D: Glycogen accumulation regulator GarA
C: UNK-UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1048
Polymers48,2873
Non-polymers8185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PknB
E: Glycogen accumulation regulator GarA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3734
Polymers47,8432
Non-polymers5302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.310, 70.460, 188.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABDE

#1: Protein Serine/threonine-protein kinase PknB


Mass: 30520.119 Da / Num. of mol.: 2 / Mutation: L33E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pknB, Rv0014c, MTCY10H4.14c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WI81, non-specific serine/threonine protein kinase
#2: Protein Glycogen accumulation regulator GarA


Mass: 17322.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: garA, Rv1827, MTCY1A11.16c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WJA9

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide UNK-UNK-UNK-UNK-UNK


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 235 molecules

#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Hepes-Na pH 7.5, 4 % w/v PEG 400, 2 M (NH4)2SO4, 4 mM AMP-PCP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.37→38.85 Å / Num. obs: 36716 / % possible obs: 96.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 67.39 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.04 / Net I/σ(I): 10.5
Reflection shellResolution: 2.37→2.46 Å / Rmerge(I) obs: 0.439 / Rpim(I) all: 0.235

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O6Y

1o6y


Resolution: 2.37→38.85 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.378 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1880 5.13 %RANDOM
Rwork0.22 ---
obs0.221 36656 95.6 %-
Displacement parametersBiso mean: 67.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.6753 Å20 Å20 Å2
2---3.8404 Å20 Å2
3---7.5158 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.37→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 148 228 6007
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.998042HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1940SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1038HARMONIC5
X-RAY DIFFRACTIONt_it5886HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion16.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion780SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6663SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.44 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2678 101 4.5 %
Rwork0.2514 2145 -
all0.2521 2246 -
obs--72.39 %
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)
13.1976-0.31940.90850.6960.33732.0965-0.06360.3622-0.161-0.25040.0503-0.10190.13920.20750.0133-0.0559-0.08020.05070.1049-0.016-0.141213.7274-19.7444-15.5426
22.0299-0.0595-0.43252.2003-0.01512.74410.03960.20380.5343-0.26280.07450.0944-0.5399-0.0489-0.1141-0.0744-0.0240.0187-0.0756-0.0018-0.0842-2.5635-1.0461-5.0768
32.1541-0.7033-0.9965.2158-0.69764.8193-0.01080.3109-0.10780.1311-0.12910.1358-0.0001-0.54420.1398-0.09210.07510.02830.0772-0.0894-0.2293-4.9544-0.515932.6724
43.98490.6477-1.28932.64851.29234.29910.1747-0.1553-0.1959-0.44650.1284-0.5442-0.28440.5286-0.3031-0.12320.02080.152-0.14830.003-0.079815.410415.870138.9062
53.9949-1.3952-1.67582.09590.3345.4815-0.1901-0.0872-0.01970.24910.1919-0.35730.1159-0.0357-0.0018-0.1630.00890.0421-0.0413-0.121-0.060313.8179-12.373520.2297
65.96182.83622.91047.09541.06998.3155-0.0161-0.2629-0.3322-0.08540.07810.10790.1252-0.2382-0.062-0.2755-0.152-0.0436-0.0354-0.0738-0.15335.77351.767569.7304
700.02930.18610.0734-0.115800.0007-0.00650.0015-0.010.0025-0.0003-0.00290.0019-0.00310.0134-0.0053-0.0475-0.00110.0231-0.009-10.7128-6.7329-23.7308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|96 }
2X-RAY DIFFRACTION2{ A|97 - A|277 }
3X-RAY DIFFRACTION3{ B|2 - B|96 }
4X-RAY DIFFRACTION4{ B|97 - B|277 }
5X-RAY DIFFRACTION5{ D|* }
6X-RAY DIFFRACTION6{ E|* }
7X-RAY DIFFRACTION7{ C|* }

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