6P7O | pdb_00006p7o

Structure of E. coli MS115-1 NucC, Apo form

• PDB DOI: https://doi.org/10.2210/pdb6P7O/pdb

• Classification: DNA BINDING PROTEIN
• 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., Lau, R.K., Berg, K.R., Corbett, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

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: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.25 kDa 
• Atom Count: 1,981 
• Modeled Residue Count: 225 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E. coli MS115-1 NucC	A	241	Escherichia coli MS 115-1	Mutation(s): 0  Gene Names: HMPREF9540_01761 EC: 3.1
UniProt
Find proteins for D7Y2H5 (Escherichia coli (strain MS 115-1)) Explore D7Y2H5  Go to UniProtKB:  D7Y2H5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	C [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.196 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/664

Diffraction Data: https://doi.org/10.15785/SBGRID/665

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 208.79	α = 90
b = 208.79	β = 90
c = 208.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Ye, Q., Lau, R.K., Berg, K.R., 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: 2024-03-13
  Changes: Data collection, Database references, Derived calculations