8XFE | pdb_00008xfe

Cryo-EM structure of defence-associated sirtuin 2 (DSR2) H171A protein in complex with DSR anti-defence 1(DSAD1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural insights into activation mechanisms on NADase of the bacterial DSR2 anti-phage defense system.

Zhang, H.Li, Y.Li, L.Chen, L.Zhu, C.Sun, L.Dong, P.Jing, D.Yang, J.Fu, L.Xiao, F.Xia, N.Li, S.Zheng, Q.Wu, Y.

(2024) Sci Adv 10: eadn5691-eadn5691

  • DOI: https://doi.org/10.1126/sciadv.adn5691
  • Primary Citation Related Structures: 
    8XEW, 8XFE, 8XFF

  • PubMed Abstract: 

    As a sirtuin (SIR2) family protein, defense-associated sirtuin2 (DSR2) has been demonstrated to participate in bacterial anti-phage resistance via depleting nicotinamide adenine dinucleotide (NAD + ) of infected cells, which can be activated by tail tube protein (TTP) and inhibited by DSR anti-defense 1 (DSAD1) of diverse phages. However, the regulating mechanism remains elusive. Here, we determined the cryo-electron microscopy structure of apo DSR2, as well as the respective complex structures with TTP and DSAD1. Structural analyses and biochemical studies reveal that DSR2 forms a tetramer with a SIR2 central core and two distinct conformations. Monomeric TTP preferentially binds to the closed conformation of DSR2, inducing conformational distortions on SIR2 tetramer assembly to activate its NADase activity. DSAD1 combines with the open conformation of DSR2, directly or allosterically inhibiting TTP activation on DSR2 NAD + hydrolysis. Our findings decipher the detailed molecule mechanisms for DSR2 NADase activity regulation and lay a foundation for in-depth understanding of the DSR2 anti-phage defense system.


  • Organizational Affiliation
    • Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou 350117, PR China.

Macromolecule Content 

  • Total Structure Weight: 487.51 kDa 
  • Atom Count: 20,339 
  • Modeled Residue Count: 2,625 
  • Deposited Residue Count: 4,135 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DSR2(H171A)
A, B, D, E
1,005Bacillus sp. DSM 5850Mutation(s): 0 
EC: 3.2.2.5
UniProt
Find proteins for P0DXN8 (Bacillus subtilis)
Explore P0DXN8 
Go to UniProtKB:  P0DXN8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DXN8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DSAD1115Phage #DMutation(s): 0 
UniProt
Find proteins for O64191 (Bacillus phage SPbeta)
Explore O64191 
Go to UniProtKB:  O64191
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO64191
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release