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- PDB-8yln: The structure of DSR2-Tail tube complex -

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Basic information

Entry
Database: PDB / ID: 8yln
TitleThe structure of DSR2-Tail tube complex
Components
  • Bacillus phage SPR Tube protein
  • SIR2-like domain-containing protein
KeywordsIMMUNE SYSTEM / Complex
Function / homology: / Uncharacterized protein
Function and homology information
Biological speciesBacillus subtilis (bacteria)
Bacillus phage SPR (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsZheng, J. / Yang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070040, 32370071 China
CitationJournal: Int J Biol Macromol / Year: 2024
Title: Structural insights into autoinhibition and activation of defense-associated sirtuin protein.
Authors: Xu Yang / Yiqun Wang / Jianting Zheng /
Abstract: Bacterial defense-associated sirtuin 2 (DSR2) proteins harbor an N-terminal sirtuin (SIR2) domain degrading NAD. DSR2 from Bacillus subtilis 29R is autoinhibited and unable to hydrolyze NAD in the ...Bacterial defense-associated sirtuin 2 (DSR2) proteins harbor an N-terminal sirtuin (SIR2) domain degrading NAD. DSR2 from Bacillus subtilis 29R is autoinhibited and unable to hydrolyze NAD in the absence of phage infection. A tail tube protein (TTP) of phage SPR activates the DSR2 while a DSR2-inhibiting protein of phage SPbeta, known as DSAD1 (DSR anti-defense 1), inactivates the DSR2. Although DSR2 structures in complexed with TTP and DSAD1, respectively, have been reported recently, the autoinhibition and activation mechanisms remain incompletely understood. Here, we present cryo-electron microscopy structures of the DSR2-NAD complex in autoinhibited state and the in vitro assembled DSR2-TFD (TTP tube-forming domain) complex in activated state. The DSR2-NAD complex reveals that the autoinhibited DSR2 assembles into an inactive tetramer, binding NAD through a distinct pocket situated outside active site. Binding of TFD into cavities within the sensor domains of DSR2 triggers a conformational change in SIR2 regions, activating its NADase activity, whereas the TTP β-sandwich domain (BSD) is flexible and does not contribute to the activation process. The activated form of DSR2 exists as tetramers and dimers, with the tetramers exhibiting more NADase activity. Overall, our results extend the current understanding of autoinhibition and activation of DSR2 immune proteins.
History
DepositionMar 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIR2-like domain-containing protein
B: SIR2-like domain-containing protein
C: Bacillus phage SPR Tube protein
D: Bacillus phage SPR Tube protein


Theoretical massNumber of molelcules
Total (without water)295,8814
Polymers295,8814
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein SIR2-like domain-containing protein


Mass: 118635.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_2870 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A162TTM4
#2: Protein Bacillus phage SPR Tube protein


Mass: 29304.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SPR (virus) / Gene: B4122_1986 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A162TY69

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of DSR2 and Tail tube / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Bacillus subtilis (bacteria)1423
21Bacillus phage SPR (virus)10725
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris bufferTris-HCl1
2150 mMSodium chlorideNaCl1
32 mMDithiothreitolDTT1
42 %GlycerolGlycerol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258165 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414484
ELECTRON MICROSCOPYf_angle_d0.60519484
ELECTRON MICROSCOPYf_dihedral_angle_d4.3661872
ELECTRON MICROSCOPYf_chiral_restr0.0382070
ELECTRON MICROSCOPYf_plane_restr0.0052496

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