6P80 | pdb_00006p80

Structure of E. coli MS115-1 CdnC + ATP

• PDB DOI: https://doi.org/10.2210/pdb6P80/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli MS 115-1
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.9 kDa 
• Atom Count: 2,876 
• Modeled Residue Count: 318 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E. coli MS115-1 NucC	A	321	Escherichia coli MS 115-1	Mutation(s): 0  Gene Names: HMPREF9540_01758 EC: 2.7.7.85 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for D7Y2H2 (Escherichia coli (strain MS 115-1)) Explore D7Y2H2  Go to UniProtKB:  D7Y2H2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/668

Diffraction Data: https://doi.org/10.15785/SBGRID/669

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.184	α = 90
b = 76.184	β = 90
c = 100.498	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Ye, Q., Azimi, C.S., 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: 2024-03-13
  Changes: Data collection, Database references, Derived calculations