8YGP

The tetramer Structure of DSR2-SPR with NAD

Summary for 8YGP

• Entry DOI: 10.2210/pdb8ygp/pdb
• EMDB information: 39259
• Descriptor: SIR2-like domain-containing protein, SPR (2 entities in total)
• Functional Keywords: sir2, nadase, spr, tetramer, hydrolase
• Biological source: Bacillus subtilis A29; More
• Total number of polymer chains: 8
• Total formula weight: 591493.71

Authors

Gao, X.,Zhu, H.,Cui, S. (deposition date: 2024-02-26, release date: 2025-03-05)

Primary citation

Zhu, K.,Shang, K.,Wang, L.,Yu, X.,Hua, L.,Zhang, W.,Qin, B.,Wang, J.,Gao, X.,Zhu, H.,Cui, S.
Activation of the bacterial defense-associated sirtuin system.
Commun Biol, 8:297-297, 2025

PubMed Abstract: The NADase activity of the defense-associated sirtuins (DSRs) is activated by the phage tail tube protein (TTP). Herein, we report cryo-EM structures of a free-state Bacillus subtilis DSR2 tetramer and a fragment of the tetramer, a phage SPR tail tube, and two DSR2-TTP complexes. DSR2 contains an N-terminal SIR2 domain, a middle domain (MID) and a C-terminal domain (CTD). The DSR2 CTD harbors the α-solenoid tandem-repeats like the HEAT-repeat proteins. DSR2 assembles into a tetramer with four SIR2 clustered at the center, and two intertwined MID-CTD chains flank the SIR2 core. SPR TTPs self-assemble into a tube-like complex. Upon DSR2 binding, the D1 domain of SPR TTP is captured between the HEAT-repeats domains of DSR2, which conflicts with TTPs self-assembly. Binding of TTPs induces conformational changes in DSR2 tetramer, resulting in increase of the NAD pocket volume in SIR2, thus activates the NADase activity and leads to cellular NAD depletion.

PubMed: 39994439
DOI: 10.1038/s42003-025-07743-3

Experimental method

ELECTRON MICROSCOPY (4.4 Å)