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- EMDB-60470: The dimer complex of DSR2 and tube-forming domain of phage tail t... -

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Basic information

Entry
Database: EMDB / ID: EMD-60470
TitleThe dimer complex of DSR2 and tube-forming domain of phage tail tube protein
Map data
Sample
  • Complex: The dimer complex of DSR2 and tube-forming domain of phage tail tube protein
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Bacillus phage SPR Tube protein
KeywordsComplex / IMMUNE SYSTEM
Function / homologySIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / Uncharacterized protein / SIR2-like domain-containing protein
Function and homology information
Biological speciesBacillus subtilis subsp. natto (strain BEST195) (bacteria) / Bacillus subtilis subsp. natto BEST195 (bacteria) / Bacillus phage SPR (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsZheng J / Yang X
Funding support China, 1 items
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
DepositionJun 7, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_60470.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.932 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-1.02472 - 1.5156837
Average (Standard dev.)0.0016362319 (±0.029987464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : The dimer complex of DSR2 and tube-forming domain of phage tail t...

EntireName: The dimer complex of DSR2 and tube-forming domain of phage tail tube protein
Components
  • Complex: The dimer complex of DSR2 and tube-forming domain of phage tail tube protein
    • Protein or peptide: SIR2-like domain-containing protein
    • Protein or peptide: Bacillus phage SPR Tube protein

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Supramolecule #1: The dimer complex of DSR2 and tube-forming domain of phage tail t...

SupramoleculeName: The dimer complex of DSR2 and tube-forming domain of phage tail tube protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. natto (strain BEST195) (bacteria)

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Macromolecule #1: SIR2-like domain-containing protein

MacromoleculeName: SIR2-like domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. natto BEST195 (bacteria)
Molecular weightTheoretical: 118.635789 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL ...String:
MVKVDLESKR YGEKLKEVFL MLDNNVVECI KEITESSRNG KLVFFVGAGV STLSDYPQWW RLVDKYHEEL YGSPKKGNYS SDEYLRIPQ IFYNVKGEMA FDGILKDFFQ VDKPTNPIHD KILAMNPAHV ITTNYDNLID TACWKRGKYF SVISAEEDVA N ATSSRYLL KVHGDFRKGF KGENVVLKED DYLNYDQNYP LISNLMKTII ATHTIVFIGY GLGDYNINML LNWVRKLQKD SF HKPFFIR TDPSPIENET LIYYENKGLR IIDAASLIDS NEYDYLERYS AVMDLLIESQ ENKFITKDDE VIDYIYGKIS PLF ALQYIR KIDLKHVFEY DYHFEVNGTV VRHKNKGFGY MERFFELKES CDERSKLSKK QYERFNALFN FFEKNGVICM AKDA GTLNT SIEINSLAYH GKYDVMKKFI EEQSVSIEDD YKKAFFLACL GRWEESYDLY SNIILNSIDE SNGCVYYLSQ INRYR IYQS ITQAVTQFNG LGLLTFGRHY KPFTDEFLAR IEREMTNFNI DDLFNGMPFE FQKKYKILEF LSDNQFLYDD TVKLFE LTN KVRSEMSEGS YSFGMSSDIV VLLRLYDNLR FLYENCLWSV SFHEFHQYIR NSMSLLIEKA EYERTRDIDE LGFSFFG KK SGFFMEYYDF VNISRHFKID DIKNLERSCS IDKIRFGEQE KIEEYLVGIA EEITKQFSAN GMNVVFYTQF ISEAKAAL Y FAKYVKLSEE GLGKIVKALL FYFPERDLDI GKRYVWLERL TKCNELPKSI ISIIDDFLVL QAEKHIDQNY SEVSSNGLY SRDYGALIKH FEKNFISKRL SEITLCLTQD KQKQIDFLFK LLPLLSTNAK SHLLSFKSVE NINDLMNGIR IGLIDEFTPE HEELIIEYL ETRKVNYIVE KEKGIQTFSS NDYMSTFGIW YFLEEINNSK MEEFIGMDDQ YDFFVDPENF DYKKFIPSWL K NYNDKLLG KIAGNKHMKH HVIEVLKERV KNSNDKRYLE ILMNYFI

UniProtKB: SIR2-like domain-containing protein

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Macromolecule #2: Bacillus phage SPR Tube protein

MacromoleculeName: Bacillus phage SPR Tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPR (virus)
Molecular weightTheoretical: 29.304701 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ...String:
MKTVIQDTAD VYFKRKSDGK LVFTAEAQTA SFSQAISEEK LRGGIGNKPL YILKSEKEIN LTVKNAFFDL EWLAMTQGET IQEETKVKV FDREHGLIVD DTNKVTLKGK PVSDVTFYNK KGLTYKIAVS TDGTYTIPTA FAAAKDKLTA VYQIEKVGRR L AIKASKFS ERYEVEYRTI AYNPDTEEVY SDIYIQFPNV SPSGEFEMSL ENGNALAPEI KFEALADTDT DEMAVVIEAS RD ENTAAPV EDTTGSTQSS DLGGTTE

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris buffer
150.0 mMNaClSodium chloride
2.0 mMDTTDithiothreitol
2.0 %GlycerolGlycerol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 385304
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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