4GLK | pdb_00004glk

Structure and activity of AbiQ, a lactococcal anti-phage endoribonuclease belonging to the type-III toxin-antitoxin system

• PDB DOI: https://doi.org/10.2210/pdb4GLK/pdb

• Classification: HYDROLASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2012-08-14 Released: 2013-01-16 
• Deposition Author(s): Samson, J., Spinelli, S., Cambillau, C., Moineau, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.223 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin-antitoxin system.

Samson, J.E., Spinelli, S., Cambillau, C., Moineau, S.

(2013) Mol Microbiol 87: 756-768

• PubMed: 23279123 
• DOI: https://doi.org/10.1111/mmi.12129
• Primary Citation Related Structures: 
  4GLK


• PubMed Abstract: 
  

  AbiQ is a phage resistance mechanism found on a native plasmid of Lactococcus lactis that abort virulent phage infections. In this study, we experimentally demonstrate that AbiQ belongs to the recently described type III toxin-antitoxin systems. When overexpressed, the AbiQ protein (ABIQ) is toxic and causes bacterial death in a bacteriostatic manner. Northern and Western blot experiments revealed that the abiQ gene is transcribed and translated constitutively, and its expression is not activated by a phage product. ABIQ is an endoribonuclease that specifically cleaves its cognate antitoxin RNA molecule in vivo. The crystal structure of ABIQ was solved and site-directed mutagenesis identified key amino acids for its anti-phage and/or its RNase function. The AbiQ system is the first lactococcal abortive infection system characterized to date at a structural level.

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Organizational Affiliation: 
• Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et génie, Université Laval, Québec, Canada, G1V 0A6.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 20.59 kDa 
• Atom Count: 1,440 
• Modeled Residue Count: 165 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AbiQ	A	172	Lactococcus lactis	Mutation(s): 1  Gene Names: abiQ EC: 3.1
UniProt
Find proteins for Q9ZJ19 (Lactococcus lactis subsp. lactis) Explore Q9ZJ19  Go to UniProtKB:  Q9ZJ19

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.223 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.14	α = 90
b = 54.51	β = 90
c = 64.24	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Samson, J., Spinelli, S., Cambillau, C., Moineau, S.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description