2LLZ | pdb_00002llz

GhoS (YjdK) monomer

• PDB DOI: https://doi.org/10.2210/pdb2LLZ/pdb
• BMRB: 18086

• Classification: UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-18 Released: 2012-09-05 
• Deposition Author(s): Lord, D., Peti, W., Page, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

A new type V toxin-antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS.

Wang, X., Lord, D.M., Cheng, H.Y., Osbourne, D.O., Hong, S.H., Sanchez-Torres, V., Quiroga, C., Zheng, K., Herrmann, T., Peti, W., Benedik, M.J., Page, R., Wood, T.K.

(2012) Nat Chem Biol 8: 855-861

• PubMed: 22941047 
• DOI: https://doi.org/10.1038/nchembio.1062
• Primary Citation Related Structures: 
  2LLZ


• PubMed Abstract: 
  

  Among bacterial toxin-antitoxin systems, to date no antitoxin has been identified that functions by cleaving toxin mRNA. Here we show that YjdO (renamed GhoT) is a membrane lytic peptide that causes ghost cell formation (lysed cells with damaged membranes) and increases persistence (persister cells are tolerant to antibiotics without undergoing genetic change). GhoT is part of a new toxin-antitoxin system with YjdK (renamed GhoS) because in vitro RNA degradation studies, quantitative real-time reverse-transcription PCR and whole-transcriptome studies revealed that GhoS masks GhoT toxicity by cleaving specifically yjdO (ghoT) mRNA. Alanine substitutions showed that Arg28 is important for GhoS activity, and RNA sequencing indicated that the GhoS cleavage site is rich in U and A. The NMR structure of GhoS indicates it is related to the CRISPR-associated-2 RNase, and GhoS is a monomer. Hence, GhoT-GhoS is to our knowledge the first type V toxin-antitoxin system where a protein antitoxin inhibits the toxin by cleaving specifically its mRNA.

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Organizational Affiliation: 
• Key Laboratory of Marine Bio-Resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.67 kDa 
• Atom Count: 820 
• Modeled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein yjdK	A	100	Escherichia coli K-12	Mutation(s): 0  Gene Names: yjdK, b4128, JW4089 EC: 3.1
UniProt
Find proteins for P0AF61 (Escherichia coli (strain K12)) Explore P0AF61  Go to UniProtKB:  P0AF61

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Lord, D., Peti, W., Page, R.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2012-09-19
  Changes: Database references
• Version 1.2: 2013-01-16
  Changes: Database references
• Version 1.3: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references