TB Genome Annotation Portal

Rv2097c (pafA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: pup-protein ligase
  • REFSEQ: hypothetical protein
  • PATRIC: Pup ligase PafA possible component of postulated heterodimer PafA-PafA'
  • TUBERCULIST: Proteasome accessory factor a PafA
  • NCBI: Proteasome accessory factor a PafA
  • updated information (H37Rv4):
    • gene name: pafA
    • function:
    • reference:
• Type: Essential
• Start: 2355319
• End: 2356677
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0071732 - cellular response to nitric oxide (Uniprot)
  • GO:0070490 - protein pupylation (Uniprot)
  • GO:0051409 - response to nitrosative stress (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0019941 - modification-dependent protein catabolic process (Uniprot)
  • GO:0019787 - ubiquitin-like protein transferase activity (Uniprot)
  • GO:0016881 - acid-amino acid ligase activity (Uniprot)
  • GO:0016879 - ligase activity, forming carbon-nitrogen bonds (Uniprot)
  • GO:0016874 - ligase activity (Uniprot)
  • GO:0010498 - proteasomal protein catabolic process (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0000166 - nucleotide 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
  4B0T	53%	CORYNEBACTERIUM GLUTAMICUM	Structure of the Pup Ligase PafA of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP
  4BJR	53%	CORYNEBACTERIUM GLUTAMICUM	Crystal structure of the complex between Prokaryotic Ubiquitin-like Protein Pup and its Ligase PafA
  5LRT	41%	Acidothermus cellulolyticus (strain ATCC 43068 / 11B)	Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ADP and Phosphate
  4B0S	41%	ACIDOTHERMUS CELLULOLYTICUS	Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway in Complex with ATP
  4B0R	41%	ACIDOTHERMUS CELLULOLYTICUS	Structure of the Deamidase-Depupylase Dop of the Prokaryotic Ubiquitin-like Modification Pathway

• Links to additional information on pafA:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.866 (from Jeremy Rock's lab)

Amino Acid Sequence

VQRRIMGIETEFGVTCTFHGHRRLSPDEVARYLFRRVVSWGRSSNVFLRNGARLYLDVGSHPEYATAECDSLVQLVTHDRAGEWVLEDLLVDAEQRLADE
GIGGDIYLFKNNTDSAGNSYGCHENYLIVRAGEFSRISDVLLPFLVTRQLICGAGKVLQTPKAATYCLSQRAEHIWEGVSSATTRSRPIINTRDEPHADA
EKYRRLHVIVGDSNMSETTTMLKVGTAALVLEMIESGVAFRDFSLDNPIRAIREVSHDVTGRRPVRLAGGRQASALDIQREYYTRAVEHLQTREPNAQIE
QVVDLWGRQLDAVESQDFAKVDTEIDWVIKRKLFQRYQDRYDMELSHPKIAQLDLAYHDIKRGRGIFDLLQRKGLAARVTTDEEIAEAVDQPPQTTRARL
RGEFISAAQEAGRDFTVDWVHLKLNDQAQRTVLCKDPFRAVDERVKRLIASM

Additional Information