TB Genome Annotation Portal

Rv3358 (relK)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: toxin
  • REFSEQ: hypothetical protein
  • PATRIC: YoeB toxin protein
  • TUBERCULIST: Toxin RelK
  • NCBI: Toxin RelK
  • updated information (H37Rv4):
    • gene name: relK
    • function: relE3?
    • reference: Singh (2010) PMID: 20061486
• Type: Not Target
• Start: 3771045
• End: 3771302
• Operon:


• Trans-membrane region:
  
• Role: VI - Unknowns
• GO terms:
  • GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
  • GO:0045892 - negative regulation of transcription, DNA-templated (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0006401 - RNA catabolic process (Uniprot)
  • GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
  • GO:0006351 - transcription, DNA-templated (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004519 - endonuclease activity (Uniprot)
  • GO:0004518 - nuclease activity (Uniprot)
  • GO:0003677 - DNA binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
• Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
• Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
• Orthologs among selected mycobacteria
• Protein structure: 3oei
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3OEI	100%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis RelJK (Rv3357-Rv3358-RelBE3)
  6OXI	49%	Escherichia coli	Dimeric E.coli YoeB bound to Thermus thermophilus 70S post-cleavage (UAA)
  6OXA	49%	Escherichia coli	Dimeric E.coli YoeB bound to Thermus thermophilus 70S pre-cleavage (AAU)
  6OTR	49%	Escherichia coli	Dimeric E.coli YoeB bound to Thermus thermophilus 70S post-cleavage (AAU)
  6NY6	49%	Escherichia coli	Structure of dimeric Escherichia coli toxin YoeB bound to the Thermus thermophilus 30S ribosome
  4V8X	49%	ESCHERICHIA COLI	Structure of Thermus thermophilus ribosome
  2A6S	49%	Escherichia coli	Crystal structure of YoeB under isopropanol condition
  2A6R	49%	Escherichia coli	Crystal structure of YoeB under PEG condition
  2A6Q	49%	Escherichia coli	Crystal structure of YefM-YoeB complex
  6N90	43%	Agrobacterium tumefaciens	YoeB/ParE toxin from Agrobacterium tumefaciens

• Links to additional information on relK:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.946 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VRSVNFDPDAWEDFLFWLAADRKTARRITRLIGEIQRDPFSGIGKPEPLQGELSGYWSRRIDDEHRLVYRAGDDEVTMLKARYHY

Additional Information

relE3
http://www.ncbi.nlm.nih.gov/pubmed/20061486

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.02 (0.07)	1.16 (0.38)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link