6Q1H | pdb_00006q1h

Structure of P. aeruginosa ATCC27853 NucC, cAAA-bound form

• PDB DOI: https://doi.org/10.2210/pdb6Q1H/pdb
• NAKB: 6Q1H

• Classification: DNA BINDING PROTEIN/RNA
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-04 Released: 2019-12-25 
• Deposition Author(s): Ye, Q., Lau, R.K., Corbett, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity.

Lau, R.K., Ye, Q., Birkholz, E.A., Berg, K.R., Patel, L., Mathews, I.T., Watrous, J.D., Ego, K., Whiteley, A.T., Lowey, B., Mekalanos, J.J., Kranzusch, P.J., Jain, M., Pogliano, J., Corbett, K.D.

(2020) Mol Cell 77: 723

• PubMed: 31932164 
• DOI: https://doi.org/10.1016/j.molcel.2019.12.010
• Primary Citation Related Structures: 
  6P7O, 6P7P, 6P7Q, 6Q1H, 6UXF, 6UXG


• PubMed Abstract: 
  

  Bacteria possess an array of defenses against foreign invaders, including a broadly distributed bacteriophage defense system termed CBASS (cyclic oligonucleotide-based anti-phage signaling system). In CBASS systems, a cGAS/DncV-like nucleotidyltransferase synthesizes cyclic di- or tri-nucleotide second messengers in response to infection, and these molecules activate diverse effectors to mediate bacteriophage immunity via abortive infection. Here, we show that the CBASS effector NucC is related to restriction enzymes but uniquely assembles into a homotrimer. Binding of NucC trimers to a cyclic tri-adenylate second messenger promotes assembly of a NucC homohexamer competent for non-specific double-strand DNA cleavage. In infected cells, NucC activation leads to complete destruction of the bacterial chromosome, causing cell death prior to completion of phage replication. In addition to CBASS systems, we identify NucC homologs in over 30 type III CRISPR/Cas systems, where they likely function as accessory nucleases activated by cyclic oligoadenylate second messengers synthesized by these systems' effector complexes.

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Organizational Affiliation: 
• 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.
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; Department of Chemistry, 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; Department of Medicine, 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 Microbiology, Harvard Medical School, Boston, MA, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
Department of Microbiology, Harvard Medical School, Boston, MA, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry, 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: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 162.01 kDa 
• Atom Count: 13,562 
• Modeled Residue Count: 1,445 
• Deposited Residue Count: 1,452 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial protein ORF C62	A, B, C, E, F, G	241	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: ORF C62 EC: 3.1
UniProt
Find proteins for P0DTF8 (Pseudomonas aeruginosa) Explore P0DTF8  Go to UniProtKB:  P0DTF8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*A)-3')	D, H	3	Pseudomonas aeruginosa

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.167 (Depositor), 0.168 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/732

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.498	α = 90
b = 80.45	β = 90
c = 262.078	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Ye, Q., Lau, R.K., 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: 2020-01-29
  Changes: Database references
• Version 1.3: 2020-03-04
  Changes: Database references
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description