7RWM

Structure of Cap5 from Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular mechanisms of the CdnG-Cap5 antiphage defense system employing 3',2'-cGAMP as the second messenger.

Fatma, S.Chakravarti, A.Zeng, X.Huang, R.H.

(2021) Nat Commun 12: 6381-6381

  • DOI: https://doi.org/10.1038/s41467-021-26738-2
  • Primary Citation of Related Structures:  
    7RWK, 7RWM, 7RWS

  • PubMed Abstract: 

    Cyclic-oligonucleotide-based antiphage signaling systems (CBASS) are diverse and abundant in bacteria. Here, we present the biochemical and structural characterization of two CBASS systems, composed of CdnG and Cap5, from Asticcacaulis sp. and Lactococcus lactis. We show that CdnG from Asticcacaulis sp. synthesizes 3',2'-cGAMP in vitro, and 3',2'-cGAMP is the biological signaling molecule that activates Cap5 for DNA degradation. Crystal structures of Cap5, together with the SAVED domain in complex with 3',2'-cGAMP, provide insight into the architecture of Cap5 as well as molecular recognition of 3',2'-cGAMP by the SAVED domain of Cap5. Amino acid conservation of the SAVED domain of Cap5, together with mutational studies, led us to propose a mechanism of Back-to-Front stacking of two SAVED domains, mediated by 3',2'-cGAMP, to activate HNH nuclease domain for DNA degradation. This study of the most abundant CBASS system provides insights into the mechanisms employed by bacteria in their conflicts against phage.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SAVED domain-containing protein
A, B, C, D
385Lactococcus cremoris subsp. cremoris IBB477Mutation(s): 0 
Gene Names: AJ89_14580
UniProt
Find proteins for A0A1E7G0A2 (Lactococcus cremoris subsp. cremoris IBB477)
Explore A0A1E7G0A2 
Go to UniProtKB:  A0A1E7G0A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E7G0A2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.772α = 90
b = 180.772β = 90
c = 93.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description