Structure of P. aeruginosa ATCC27853 CdnD D62N/D64N mutant bound to ATP

Experimental Data Snapshot

  • Resolution: 1.47 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

Starting Model: experimental
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HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.

Ye, Q.Lau, R.K.Mathews, I.T.Birkholz, E.A.Watrous, J.D.Azimi, C.S.Pogliano, J.Jain, M.Corbett, K.D.

(2020) Mol Cell 77: 709

  • DOI: https://doi.org/10.1016/j.molcel.2019.12.009
  • Primary Citation of Related Structures:  
    6P80, 6P82, 6P8J, 6P8O, 6P8P, 6P8R, 6P8S, 6P8U, 6P8V, 6PB3, 6U7B

  • PubMed Abstract: 

    Bacteria are continually challenged by foreign invaders, including bacteriophages, and have evolved a variety of defenses against these invaders. Here, we describe the structural and biochemical mechanisms of a bacteriophage immunity pathway found in a broad array of bacteria, including E. coli and Pseudomonas aeruginosa. This pathway uses eukaryotic-like HORMA domain proteins that recognize specific peptides, then bind and activate a cGAS/DncV-like nucleotidyltransferase (CD-NTase) to generate a cyclic triadenylate (cAAA) second messenger; cAAA in turn activates an endonuclease effector, NucC. Signaling is attenuated by a homolog of the AAA+ ATPase Pch2/TRIP13, which binds and disassembles the active HORMA-CD-NTase complex. When expressed in non-pathogenic E. coli, this pathway confers immunity against bacteriophage λ through an abortive infection mechanism. Our findings reveal the molecular mechanisms of a bacterial defense pathway integrating a cGAS-like nucleotidyltransferase with HORMA domain proteins for threat sensing through protein detection and negative regulation by a Trip13 ATPase.

  • Organizational Affiliation

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NucleotidyltransferaseA [auth C],
B [auth A],
C [auth B],
302Pseudomonas aeruginosaMutation(s): 2 
Gene Names: DY979_07585EGY23_20895IPC669_24880PA5486_02902PAERUG_E15_London_28_01_14_04351PAMH19_6112
Find proteins for P0DTF7 (Pseudomonas aeruginosa)
Explore P0DTF7 
Go to UniProtKB:  P0DTF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTF7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ATP

Download Ideal Coordinates CCD File 
E [auth C],
H [auth A],
K [auth B],
N [auth D]
C10 H16 N5 O13 P3
Query on CL

Download Ideal Coordinates CCD File 
F [auth C],
I [auth A],
L [auth B],
O [auth D]
Query on MG

Download Ideal Coordinates CCD File 
G [auth C],
J [auth A],
M [auth B],
P [auth D]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.484α = 90
b = 152.166β = 90.12
c = 88.255γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description