6P8U

Structure of P. aeruginosa ATCC27853 CdnD:HORMA2:Peptide 1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2019) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2019.12.009
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA; Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA. Electronic address: kcorbett@ucsd.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleotidyltransferase
A
300Pseudomonas aeruginosaMutation(s): 0 
Find proteins for A0A080VY32 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A080VY32
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HORMA domain containing protein
B
166Pseudomonas aeruginosaMutation(s): 0 
Gene Names: ORF C60
Find proteins for Q8GQ50 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8GQ50
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide 1
C
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/679 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 169.087α = 90.00
b = 43.373β = 104.18
c = 63.217γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-08 
  • Released Date: 2019-12-25 
  • Deposition Author(s): Ye, Q., Corbett, K.D.

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references