6P8J | pdb_00006p8j

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

• PDB DOI: https://doi.org/10.2210/pdb6P8J/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-07 Released: 2019-12-25 
• Deposition Author(s): Ye, Q., Corbett, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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.

(2020) Mol Cell 77: 709

• PubMed: 31932165 
• DOI: https://doi.org/10.1016/j.molcel.2019.12.009
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Cellular and Molecular 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; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.
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 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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 139.08 kDa 
• Atom Count: 11,260 
• Modeled Residue Count: 1,200 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyltransferase	A [auth C], B [auth A], C [auth B], D	302	Pseudomonas aeruginosa	Mutation(s): 2  Gene Names: DY979_07585, EGY23_20895, IPC669_24880, PA5486_02902, PAERUG_E15_London_28_01_14_04351, PAMH19_6112 EC: 2.7.7.85 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P0DTF7 (Pseudomonas aeruginosa) Explore P0DTF7  Go to UniProtKB:  P0DTF7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth C], H [auth A], K [auth B], N [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CL	F [auth C], I [auth A], L [auth B], O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	G [auth C], J [auth A], M [auth B], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/671

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.484	α = 90
b = 152.166	β = 90.12
c = 88.255	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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