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- PDB-7ssj: Crystal structure of the DesK-DesR complex in the phosphatase state -

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Basic information

Entry
Database: PDB / ID: 7ssj
TitleCrystal structure of the DesK-DesR complex in the phosphatase state
Components
  • Sensor histidine kinase DesK
  • Transcriptional regulatory protein DesR
KeywordsTRANSFERASE / TWO-COMPONENT REGULATORY SYSTEM / KINASE / RESPONSE REGULATOR / PHOSPHATASE COMPLEX / DEPHOSPHORYLATION / TRANSFERASE-GENE REGULATION COMPLEX
Function / homology
Function and homology information


phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / protein kinase activity / protein dimerization activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding ...phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / protein kinase activity / protein dimerization activity / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / : / DesK N-terminal domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1930 / : / DesK N-terminal domain / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / : / Histidine kinase / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Histidine kinase/HSP90-like ATPase superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / BERYLLIUM TRIFLUORIDE ION / Transcriptional regulatory protein DesR / Sensor histidine kinase DesK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsTrajtenberg, F. / Buschiazzo, A.
Funding supportUruguay, 1items
OrganizationGrant numberCountry
Agencia Nacional de Investigacion e Innovacion (ANII)FCE_1_2017_1_136291Uruguay
Citation
Journal: Sci.Signal. / Year: 2023
Title: An allosteric switch ensures efficient unidirectional information transmission by the histidine kinase DesK from Bacillus subtilis.
Authors: Lima, S. / Blanco, J. / Olivieri, F. / Imelio, J.A. / Nieves, M. / Carrion, F. / Alvarez, B. / Buschiazzo, A. / Marti, M.A. / Trajtenberg, F.
#1: Journal: Elife / Year: 2016
Title: Regulation of signaling directionality revealed by 3D snapshots of a kinase:regulator complex in action.
Authors: Trajtenberg, F. / Imelio, J.A. / Machado, M.R. / Larrieux, N. / Marti, M.A. / Obal, G. / Mechaly, A.E. / Buschiazzo, A.
History
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionNov 16, 2022ID: 5IUN
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: 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 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor histidine kinase DesK
B: Transcriptional regulatory protein DesR
C: Sensor histidine kinase DesK
D: Sensor histidine kinase DesK
E: Transcriptional regulatory protein DesR
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,88419
Polymers121,9286
Non-polymers1,95613
Water39622
1
A: Sensor histidine kinase DesK
B: Transcriptional regulatory protein DesR
hetero molecules

A: Sensor histidine kinase DesK
B: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,52512
Polymers81,2854
Non-polymers1,2408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11370 Å2
ΔGint-80 kcal/mol
Surface area30980 Å2
MethodPISA
2
C: Sensor histidine kinase DesK
D: Sensor histidine kinase DesK
E: Transcriptional regulatory protein DesR
F: Transcriptional regulatory protein DesR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,62113
Polymers81,2854
Non-polymers1,3369
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-108 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.691, 94.691, 240.85
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 6 molecules ACDBEF

#1: Protein Sensor histidine kinase DesK


Mass: 25534.373 Da / Num. of mol.: 3 / Fragment: Fragment: entire cytoplasmic region / Mutation: S150I,S153L,R157I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: desK, yocF, BSU19190 / Production host: Escherichia coli (E. coli) / References: UniProt: O34757, histidine kinase
#2: Protein Transcriptional regulatory protein DesR


Mass: 15108.367 Da / Num. of mol.: 3 / Fragment: Receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: desR, yocG, BSU19200 / Production host: Escherichia coli (E. coli) / References: UniProt: O34723

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Non-polymers , 5 types, 35 molecules

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


Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, PEG600, MgCl2, Tris, MES, Li2SO4, MgSO4, Glycerol, 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: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.52→82.01 Å / Num. obs: 34302 / % possible obs: 79.6 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.085 / Net I/σ(I): 21.3
Reflection shellResolution: 2.52→2.73 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1709 / CC1/2: 0.502 / % possible all: 18.9

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20191129data processing
Aimless0.7.4data scaling
BUSTER2.10.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IUN

5iun
PDB Unreleased entry


Resolution: 2.52→82 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 1.418 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.328 / SU Rfree Blow DPI: 0.373 / SU Rfree Cruickshank DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1720 -RANDOM
Rwork0.2533 ---
obs0.2551 34302 79.3 %-
Displacement parametersBiso mean: 104.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.4929 Å20 Å20 Å2
2--1.4929 Å20 Å2
3----2.9858 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.52→82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7955 0 116 22 8093
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088156HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3004SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1428HARMONIC5
X-RAY DIFFRACTIONt_it8045HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1128SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance36HARMONIC1
X-RAY DIFFRACTIONt_utility_angle41HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact6167SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion19.07
LS refinement shellResolution: 2.52→2.67 Å
RfactorNum. reflection% reflection
Rfree0.3559 38 -
Rwork0.3312 --
obs0.3326 687 10.36 %
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)
11.92671.4095-0.97483.4573-0.758900.09690.4693-0.0360.4693-0.07860.2616-0.0360.2616-0.01840.3353-0.5328-0.1736-0.01020.0938-0.1243-14.4079-23.97153.5847
24.85390.5643-0.65244.40640.67565.5559-0.38720.2618-0.24940.26180.2349-0.0232-0.2494-0.02320.15230.2415-0.2426-0.1509-0.13230.002-0.1992-13.5317-28.58726.3183
35.5818-4.09755.139-2.5514-0.20472.1058-0.16820.17560.30570.17560.07960.25050.30570.25050.08850.2823-0.2885-0.027-0.0210.034-0.0146-5.3549-52.92261.2975
41.2607-0.4072-0.05430.0276-0.33380.8083-0.72470.0760.36140.0760.2812-0.16080.3614-0.16080.44350.0855-0.27270.27750.0698-0.35310.039723.8038-74.811127.7094
55.9080.90592.88256.64892.04435.2391-0.0069-1.4420.4875-1.442-0.03910.48910.48750.48910.0460.2722-0.1650.59730.1092-0.1816-0.294120.7788-68.41930.6326
65.14853.05821.2453.4735-1.070911.4201-0.513-0.36530.108-0.3653-0.20920.3570.1080.3570.7222-0.31530.14660.34830.02460.19810.070817.0187-78.279553.2564
7-3.34622.95491.81365.1050.8892.377-0.21290.0081-0.43730.00810.1259-0.2773-0.4373-0.27730.0870.2616-0.22510.02210.0811-0.0190.131711.6889-47.011428.1928
8-0.0163-1.37820.83575.32224.60-0.00270.1203-0.18790.1203-0.0015-0.2518-0.1879-0.25180.00420.258-0.18620.1315-0.1672-0.17870.2583-5.2353-88.741726.6931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|151 - A|243 }A151 - 243
2X-RAY DIFFRACTION2{ A|244 - A|369 A|401 - A|402 A|503 - A|503 }A244 - 369
3X-RAY DIFFRACTION2{ A|244 - A|369 A|401 - A|402 A|503 - A|503 }A401 - 402
4X-RAY DIFFRACTION2{ A|244 - A|369 A|401 - A|402 A|503 - A|503 }A503
5X-RAY DIFFRACTION3{ A|501 - A|501 B|303 - B|303 B|302 - B|302 }A501
6X-RAY DIFFRACTION3{ A|501 - A|501 B|303 - B|303 B|302 - B|302 }B303
7X-RAY DIFFRACTION3{ A|501 - A|501 B|303 - B|303 B|302 - B|302 }B302
8X-RAY DIFFRACTION4{ C|150 - C|243 D|149 - D|243 }C150 - 243
9X-RAY DIFFRACTION4{ C|150 - C|243 D|149 - D|243 }D149 - 243
10X-RAY DIFFRACTION5{ C|244 - C|369 C|401 - C|402 C|502 - C|502 }C244 - 369
11X-RAY DIFFRACTION5{ C|244 - C|369 C|401 - C|402 C|502 - C|502 }C401 - 402
12X-RAY DIFFRACTION5{ C|244 - C|369 C|401 - C|402 C|502 - C|502 }C502
13X-RAY DIFFRACTION6{ D|244 - D|369 D|401 - D|402 D|502 - D|502 }D244 - 369
14X-RAY DIFFRACTION6{ D|244 - D|369 D|401 - D|402 D|502 - D|502 }D401 - 402
15X-RAY DIFFRACTION6{ D|244 - D|369 D|401 - D|402 D|502 - D|502 }D502
16X-RAY DIFFRACTION7{ C|501 - C|501 E|304 - E|304 E|302 - E|302 }C501
17X-RAY DIFFRACTION7{ C|501 - C|501 E|304 - E|304 E|302 - E|302 }E304
18X-RAY DIFFRACTION7{ C|501 - C|501 E|304 - E|304 E|302 - E|302 }E302
19X-RAY DIFFRACTION8{ D|503 - D|503 F|301 - F|301 }D503
20X-RAY DIFFRACTION8{ D|503 - D|503 F|301 - F|301 }F301

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