Structure of Enterobacter cloacae Cap2 bound to CdnD02 C-terminus, Apo state

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


An E1-E2 fusion protein primes antiviral immune signalling in bacteria.

Ledvina, H.E.Ye, Q.Gu, Y.Sullivan, A.E.Quan, Y.Lau, R.K.Zhou, H.Corbett, K.D.Whiteley, A.T.

(2023) Nature 616: 319-325

  • DOI: https://doi.org/10.1038/s41586-022-05647-4
  • Primary Citation of Related Structures:  
    7TO3, 7TQD, 7TSQ, 7TSX

  • PubMed Abstract: 

    In all organisms, innate immune pathways sense infection and rapidly activate potent immune responses while avoiding inappropriate activation (autoimmunity). In humans, the innate immune receptor cyclic GMP-AMP synthase (cGAS) detects viral infection to produce the nucleotide second messenger cyclic GMP-AMP (cGAMP), which initiates stimulator of interferon genes (STING)-dependent antiviral signalling 1 . Bacteria encode evolutionary predecessors of cGAS called cGAS/DncV-like nucleotidyltransferases 2 (CD-NTases), which detect bacteriophage infection and produce diverse nucleotide second messengers 3 . How bacterial CD-NTase activation is controlled remains unknown. Here we show that CD-NTase-associated protein 2 (Cap2) primes bacterial CD-NTases for activation through a ubiquitin transferase-like mechanism. A cryo-electron microscopy structure of the Cap2-CD-NTase complex reveals Cap2 as an all-in-one ubiquitin transferase-like protein, with distinct domains resembling eukaryotic E1 and E2 proteins. The structure captures a reactive-intermediate state with the CD-NTase C terminus positioned in the Cap2 E1 active site and conjugated to AMP. Cap2 conjugates the CD-NTase C terminus to a target molecule that primes the CD-NTase for increased cGAMP production. We further demonstrate that a specific endopeptidase, Cap3, balances Cap2 activity by cleaving CD-NTase-target conjugates. Our data demonstrate that bacteria control immune signalling using an ancient, minimized ubiquitin transferase-like system and provide insight into the evolution of the E1 and E2 machinery across domains of life.

  • Organizational Affiliation

    Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
233Enterobacter cloacaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic AMP-AMP-GMP synthase
C, D
12Enterobacter cloacaeMutation(s): 0 
Gene Names: cdnD02P853_02262
EC: 2.7.7
Find proteins for P0DSP4 (Enterobacter hormaechei subsp. hoffmannii (strain UCI 50))
Explore P0DSP4 
Go to UniProtKB:  P0DSP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DSP4
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.262α = 90
b = 76.546β = 90
c = 127.631γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM104141
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI148814

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-02-22
    Changes: Database references
  • Version 1.3: 2023-04-26
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description