TB Genome Annotation Portal

Rv3100c (smpB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: SsrA-binding protein
  • REFSEQ: SsrA-binding protein
  • PATRIC: tmRNA-binding protein SmpB
  • TUBERCULIST: Probable SSRA-binding protein SmpB
  • NCBI: Probable SSRA-binding protein SmpB
  • updated information (H37Rv4):
    • gene name: smpB
    • function:
    • reference:
• Type: Not Target
• Start: 3469301
• End: 3469783
• Operon:


• Trans-membrane region:
  
• Role: IV.A - Virulence
• GO terms:
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003723 - RNA 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:
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  5ZEY	76%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	M. smegmatis Trans-translation state 70S ribosome
  4V6T	53%	Escherichia coli	Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading
  3IZ4	53%	Escherichia coli	Modified E. coli tmRNA in the resume state with the tRNA-like domain in the ribosomal P site interacting with the SmpB
  2CZJ	53%	Thermus thermophilus	Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8
  1WJX	53%	Thermus thermophilus	Crystal sturucture of TT0801 from Thermus thermophilus
  1ZC8	50%	Thermus thermophilus	Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex
  6Q95	50%	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Structure of tmRNA SmpB bound in A site of T. thermophilus 70S ribosome
  4V8Q	50%	Thermus thermophilus HB8	Complex of SmpB, a tmRNA fragment and EF-Tu-GDP-Kirromycin with the 70S ribosome
  3IYR	50%	Thermus thermophilus	tmRNA-SmpB: a journey to the center of the bacterial ribosome
  3IYQ	50%	Thermus thermophilus	tmRNA-SmpB: a journey to the center of the bacterial ribosome

• Links to additional information on smpB:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -7.993 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VSKSSRGGRQIVASNRKARHNYSIIEVFEAGVALQGTEVKSLREGQASLADSFATIDDGEVWLRNAHIPEYRHGSWTNHEPRRNRKLLLHRRQIDTLVGK
IREGNFALVPLSLYFAEGKVKVELALARGKQARDKRQDMARRDAQREVLRELGRRAKGMT

Additional Information