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TitleStructural insights into autoinhibition and activation of defense-associated sirtuin protein.
Journal, issue, pagesInt J Biol Macromol, Vol. 277, Issue Pt 1, Page 134145, Year 2024
Publish dateJul 24, 2024
AuthorsXu Yang / Yiqun Wang / Jianting Zheng /
PubMed AbstractBacterial 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.
External linksInt J Biol Macromol / PubMed:39059542
MethodsEM (single particle)
Resolution2.9 - 9.74 Å
Structure data

EMDB-39369, PDB-8ykf:
The DSR2-DSAD1 complex with DSAD1 on the opposite sides
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-39380: Local map of DSR2-DSAD1 complex
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-39381: Overall map of DSR2-DSAD1 complex
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-39382, PDB-8yl5:
The DSR2-DSAD1 complex with DSAD1 on the same sides
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-39385, PDB-8yln:
The structure of DSR2-Tail tube complex
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-39386: The loacl refined map of DSR2 and NAD structure
Method: EM (single particle) / Resolution: 9.74 Å

EMDB-39387: The local refined map of DSR2 N-terminal domains
Method: EM (single particle) / Resolution: 2.92 Å

EMDB-39390, PDB-8ylt:
The structure of DSR2 and NAD+ complex
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-39718, PDB-8z18:
The tetramer complex of DSR2 and tube-forming domain of phage tail tube protein
Method: EM (single particle) / Resolution: 3.94 Å

EMDB-60470, PDB-8ztr:
The dimer complex of DSR2 and tube-forming domain of phage tail tube protein
Method: EM (single particle) / Resolution: 3.26 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

Source
  • bacillus subtilis (bacteria)
  • bacillus phage spbc2 (virus)
  • bacillus phage spbeta (virus)
  • bacillus phage spr (virus)
  • bacillus subtilis subsp. natto (strain best195) (bacteria)
  • bacillus subtilis subsp. natto best195 (bacteria)
KeywordsIMMUNE SYSTEM / Complex

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