8YHX | pdb_00008yhx

Cryo-EM structure of the trimeric HerA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YHX

This is version 1.1 of the entry. See complete history

Literature

Mechanistic basis for the allosteric activation of NADase activity in the Sir2-HerA antiphage defense system.

Zhen, X.Zhou, B.Liu, Z.Wang, X.Zhao, H.Wu, S.Li, Z.Liang, J.Zhang, W.Zhu, Q.He, J.Xiong, X.Ouyang, S.

(2024) Nat Commun 15: 9269-9269

  • DOI: https://doi.org/10.1038/s41467-024-53614-6
  • Primary Citation Related Structures: 
    8YHO, 8YHX

  • PubMed Abstract: 

    Sir2-HerA is a widely distributed antiphage system composed of a RecA-like ATPase (HerA) and an effector with potential NADase activity (Sir2). Sir2-HerA is believed to provide defense against phage infection in Sir2-dependent NAD + depletion to arrest the growth of infected cells. However, the detailed mechanism underlying its antiphage activity remains largely unknown. Here, we report functional investigations of Sir2-HerA from Staphylococcus aureus (SaSir2-HerA), unveiling that the NADase function of SaSir2 can be allosterically activated by the binding of SaHerA, which then assembles into a supramolecular complex with NADase activity. By combining the cryo-EM structure of SaSir2-HerA in complex with the NAD + cleavage product, it is surprisingly observed that Sir2 protomers that interact with HerA are in the activated state, which is due to the opening of the α15-helix covering the active site, allowing NAD + to access the catalytic pocket for hydrolysis. In brief, our study provides a comprehensive view of an allosteric activation mechanism for Sir2 NADase activity in the Sir2-HerA immune system.


  • Organizational Affiliation
    • Kev Laboratory of Microbial Pathogenesis and Interventions of Fuian Province University, the Key Laboratory of inmate lmmune Biology of Fuijian Province, Biomedical Research Center of South China, Key Laboratory of Opto Electronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.

Macromolecule Content 

  • Total Structure Weight: 1,003.41 kDa 
  • Atom Count: 69,979 
  • Modeled Residue Count: 8,427 
  • Deposited Residue Count: 8,508 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DUF87 domain-containing protein
A, B, C, D, E
A, B, C, D, E, F
562Staphylococcus aureusMutation(s): 0 
Gene Names: GO782_01940
UniProt
Find proteins for C1PH94 (Staphylococcus aureus)
Explore C1PH94 
Go to UniProtKB:  C1PH94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1PH94
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SIR2 family protein
G, H, I, J, K
G, H, I, J, K, L, M, N, O, P, Q, R
428Staphylococcus aureusMutation(s): 0 
Gene Names: GO782_01935
UniProt
Find proteins for C1PH93 (Staphylococcus aureus)
Explore C1PH93 
Go to UniProtKB:  C1PH93
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC1PH93
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998:

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China321700145

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references