Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	The structural basis of the activation and inhibition of DSR2 NADase by phage proteins.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 6185, Year 2024
Publish date	Jul 23, 2024
Authors	Ruiwen Wang / Qi Xu / Zhuoxi Wu / Jialu Li / Hao Guo / Tianzhui Liao / Yuan Shi / Ling Yuan / Haishan Gao / Rong Yang / Zhubing Shi / Faxiang Li /
PubMed Abstract	DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while ...DSR2, a Sir2 domain-containing protein, protects bacteria from phage infection by hydrolyzing NAD. The enzymatic activity of DSR2 is triggered by the SPR phage tail tube protein (TTP), while suppressed by the SPbeta phage-encoded DSAD1 protein, enabling phages to evade the host defense. However, the molecular mechanisms of activation and inhibition of DSR2 remain elusive. Here, we report the cryo-EM structures of apo DSR2, DSR2-TTP-NAD and DSR2-DSAD1 complexes. DSR2 assembles into a head-to-head tetramer mediated by its Sir2 domain. The C-terminal helical regions of DSR2 constitute four partner-binding cavities with opened and closed conformation. Two TTP molecules bind to two of the four C-terminal cavities, inducing conformational change of Sir2 domain to activate DSR2. Furthermore, DSAD1 competes with the activator for binding to the C-terminal cavity of DSR2, effectively suppressing its enzymatic activity. Our results provide the mechanistic insights into the DSR2-mediated anti-phage defense system and DSAD1-dependent phage immune evasion.
External links	Nat Commun / PubMed:39039073 / PubMed Central
Methods	EM (single particle)
Resolution	3.11 - 4.14 Å
Structure data	38824 8y13 EMDB-38824, PDB-8y13: Cryo-EM structure of anti-phage defense associated DSR2 tetramer (H171A) Method: EM (single particle) / Resolution: 3.18 Å EMDB-38867: The Cryo-EM map of anti-phage defense associated DSR2 tetramer (H171A) Method: EM (single particle) / Resolution: 3.18 Å EMDB-38868: Local refinement of anti-phage defense associated DSR2 tetramer (H171A) Method: EM (single particle) / Resolution: 3.3 Å EMDB-38869: Local refinement of anti-phage defense associated DSR2 tetramer (H171A) Method: EM (single particle) / Resolution: 3.52 Å EMDB-38870: The Cryo-EM map of anti-phage defense associated DSR2 (H171A) before local refinement (map2) Method: EM (single particle) / Resolution: 3.11 Å EMDB-38871: Local refinement of anti-phage defense associated DSR2 (H171A) (map2) Method: EM (single particle) / Resolution: 3.14 Å 38872 8y34 EMDB-38872, PDB-8y34: Cryo-EM structure of anti-phage defense associated DSR2 (H171A) (map2) Method: EM (single particle) / Resolution: 3.11 Å EMDB-38887: The Cryo-EM map of DSR2-DSAD1 complex (cross-linked) before local refinement Method: EM (single particle) / Resolution: 3.25 Å EMDB-38888: Local refinement of DSR2-DSAD1 complex (cross-linked) Method: EM (single particle) / Resolution: 3.2 Å 38889 8y3m EMDB-38889, PDB-8y3m: Cryo-EM structure of DSR2-DSAD1 complex (cross-linked) Method: EM (single particle) / Resolution: 3.25 Å EMDB-38890: The Cryo-EM map of DSR2 tetramer bound with two DSAD1 inhibitor on the same side before local refinement Method: EM (single particle) / Resolution: 3.49 Å EMDB-38891: Local refinement of DSR2 tetramer bound with two DSAD1 inhibitor on the same side Method: EM (single particle) / Resolution: 3.37 Å EMDB-38901: Local refinement of DSR2 tetramer bound with two DSAD1 inhibitor on the same side Method: EM (single particle) / Resolution: 3.39 Å 38902 8y3w EMDB-38902, PDB-8y3w: The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (same side) Method: EM (single particle) / Resolution: 3.49 Å 38907 8y3y EMDB-38907, PDB-8y3y: The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side) Method: EM (single particle) / Resolution: 3.33 Å EMDB-39912: The cryo-EM map of DSR2-tail tube-NAD complex before local refinement Method: EM (single particle) / Resolution: 4.14 Å EMDB-39913: Local refinement of DSR2-tail tube-NAD+ complex Method: EM (single particle) / Resolution: 3.17 Å EMDB-39914: Local refinement of DSR2-tail tube-NAD+ complex Method: EM (single particle) / Resolution: 3.4 Å 39925 8zc9 EMDB-39925, PDB-8zc9: The Cryo-EM structure of DSR2-Tail tube-NAD+ complex Method: EM (single particle) / Resolution: 3.14 Å
Chemicals	ChemComp-NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM
Source	bacillus subtilis (bacteria) Bacillus subtilis
Keywords	IMMUNE SYSTEM / NADase / anti-phage defense / tetramer / IMMUNOSUPPRESSANT / complex / immune evasion / tail-tube protein / NAD