TB Genome Annotation Portal

Rv2111c (pup)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: prokaryotic ubiquitin-like protein Pup
  • REFSEQ: hypothetical protein
  • PATRIC: Prokaryotic ubiquitin-like protein Pup
  • TUBERCULIST: Prokaryotic ubiquitin-like protein Pup
  • NCBI: Prokaryotic ubiquitin-like protein Pup
  • updated information (H37Rv4):
    • gene name: pup
    • function:
    • reference:
• Type: Not Target
• Start: 2370598
• End: 2370792
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0070628 - proteasome binding (Uniprot)
  • GO:0070490 - protein pupylation (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0031386 - protein tag (Uniprot)
  • GO:0019941 - modification-dependent protein catabolic process (Uniprot)
  • GO:0010498 - proteasomal protein catabolic process (Uniprot)
  • GO:0005515 - protein 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: 3m9d, 3m91
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3M9D	98%	Mycobacterium tuberculosis	Crystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the hexameric proteasomal ATPase Mpa which includes the amino terminal coiled coil domain and the inter domain
  3M91	97%	Mycobacterium tuberculosis	Crystal structure of the prokaryotic ubiquitin-like protein (Pup) complexed with the amino terminal coiled coil of the Mycobacterium tuberculosis proteasomal ATPase Mpa
  4BJR	76%	CORYNEBACTERIUM GLUTAMICUM	Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA

• Links to additional information on pup:
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology
  • Mycobrowser
  • PATRIC
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -4.791 (from Jeremy Rock's lab)

Amino Acid Sequence

MAQEQTKRGGGGGDDDDIAGSTAAGQERREKLTEETDDLLDEIDDVLEENAEDFVRAYVQKGGQ

Additional Information

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)	0.81 (0.07)	0.47 (0.07)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link