8BB1

T3 SAM lyase in complex with S-adenosylmethionine synthase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase.

Andriianov, A.Triguis, S.Drobiazko, A.Sierro, N.Ivanov, N.V.Selmer, M.Severinov, K.Isaev, A.

(2023) Cell Rep 42: 112972-112972

  • DOI: https://doi.org/10.1016/j.celrep.2023.112972
  • Primary Citation of Related Structures:  
    8BB1

  • PubMed Abstract: 

    Bacteriophage T3 encodes a SAMase that, through cleavage of S-adenosyl methionine (SAM), circumvents the SAM-dependent type I restriction-modification (R-M) defense. We show that SAMase also allows T3 to evade the BREX defense. Although SAM depletion weakly affects BREX methylation, it completely inhibits the defensive function of BREX, suggesting that SAM could be a co-factor for BREX-mediated exclusion of phage DNA, similar to its anti-defense role in type I R-M. The anti-BREX activity of T3 SAMase is mediated not just by enzymatic degradation of SAM but also by direct inhibition of MetK, the host SAM synthase. We present a 2.8 Å cryoelectron microscopy (cryo-EM) structure of the eight-subunit T3 SAMase-MetK complex. Structure-guided mutagenesis reveals that this interaction stabilizes T3 SAMase in vivo, further stimulating its anti-BREX activity. This work provides insights in the versatility of bacteriophage counterdefense mechanisms and highlights the role of SAM as a co-factor of diverse bacterial immunity systems.


  • Organizational Affiliation

    Skolkovo Institute of Science and Technology, Moscow 143028, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase
A, B, C, D
384Escherichia coliMutation(s): 0 
EC: 2.5.1.6
UniProt
Find proteins for P0A817 (Escherichia coli (strain K12))
Explore P0A817 
Go to UniProtKB:  P0A817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A817
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S-Adenosylmethionine lyase
E, F, G, H
158Enterobacteria phage T3Mutation(s): 0 
EC: 2.5.1.4
UniProt
Find proteins for P07693 (Enterobacteria phage T3)
Explore P07693 
Go to UniProtKB:  P07693
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07693
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-03827
Knut and Alice Wallenberg FoundationSwedenEvolution of new genes and proteins

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release