SspE crystal structure

Experimental Data Snapshot

  • Resolution: 3.31 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.406 
  • R-Value Observed: 0.408 

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This is version 1.2 of the entry. See complete history


SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities.

Xiong, X.Wu, G.Wei, Y.Liu, L.Zhang, Y.Su, R.Jiang, X.Li, M.Gao, H.Tian, X.Zhang, Y.Hu, L.Chen, S.Tang, Y.Jiang, S.Huang, R.Li, Z.Wang, Y.Deng, Z.Wang, J.Dedon, P.C.Chen, S.Wang, L.

(2020) Nat Microbiol 5: 917-928

  • DOI: https://doi.org/10.1038/s41564-020-0700-6
  • Primary Citation of Related Structures:  
    6JIV, 6JUF, 6LB9

  • PubMed Abstract: 

    Bacteria have evolved diverse mechanisms to fend off predation by bacteriophages. We previously identified the Dnd system, which uses DndABCDE to insert sulfur into the DNA backbone as a double-stranded phosphorothioate (PT) modification, and DndFGH, a restriction component. Here, we describe an unusual SspABCD-SspE PT system in Vibrio cyclitrophicus, Escherichia coli and Streptomyces yokosukanensis, which has distinct genetic organization, biochemical functions and phenotypic behaviour. SspABCD confers single-stranded and high-frequency PTs with SspB acting as a nickase and possibly introducing nicks to facilitate sulfur incorporation. Strikingly, SspABCD coupled with SspE provides protection against phages in unusual ways: (1) SspE senses sequence-specific PTs by virtue of its PT-stimulated NTPase activity to exert its anti-phage activity, and (2) SspE inhibits phage propagation by introducing nicking damage to impair phage DNA replication. These results not only expand our knowledge about the diversity and functions of DNA PT modification but also enhance our understanding of the known arsenal of defence systems.

  • Organizational Affiliation

    Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SspE proteinA [auth D],
B [auth A],
C [auth B],
D [auth C]
771Streptomyces yokosukanensisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A [auth D],
B [auth A],
C [auth B],
D [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.31 Å
  • R-Value Free: 0.435 
  • R-Value Work: 0.406 
  • R-Value Observed: 0.408 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.07α = 90
b = 138.16β = 90
c = 293.68γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references