TB Genome Annotation Portal

Rv1638 (uvrA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: UvrABC system protein A
  • REFSEQ: excinuclease ABC subunit A
  • PATRIC: Excinuclease ABC subunit A
  • TUBERCULIST: Probable excinuclease ABC (subunit A - DNA-binding ATPase) UvrA
  • NCBI: Probable excinuclease ABC (subunit A-DNA-binding ATPase) UvrA
  • updated information (H37Rv4):
    • gene name: uvrA
    • function:
    • reference:
• Type: Not Target
• Start: 1843741
• End: 1846659
• Operon:


• Trans-membrane region:
  
• Role: II.A.5 - DNA replication, repair, recombination and restriction/modification
• GO terms:
  • GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
  • GO:0060543 - negative regulation of strand invasion (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0016887 - ATPase activity (Uniprot)
  • GO:0009432 - SOS response (Uniprot)
  • GO:0009381 - excinuclease ABC activity (Uniprot)
  • GO:0009380 - excinuclease repair complex (Uniprot)
  • GO:0006974 - cellular response to DNA damage stimulus (Uniprot)
  • GO:0006289 - nucleotide-excision repair (Uniprot)
  • GO:0006281 - DNA repair (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004518 - nuclease activity (Uniprot)
  • GO:0003677 - DNA 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: 3zqj
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3ZQJ	99%	MYCOBACTERIUM TUBERCULOSIS	Mycobacterium tuberculosis UvrA
  3UWX	59%	Geobacillus	Crystal structure of UvrA-UvrB complex
  2R6F	59%	Geobacillus stearothermophilus	Crystal Structure of Bacillus stearothermophilus UvrA
  3PIH	53%	Thermotoga maritima	T. maritima UvrA in complex with fluorescein-modified DNA
  4DFC	50%	Escherichia coli	Core UvrA/TRCF complex
  3UX8	46%	Geobacillus	Crystal structure of UvrA
  3FPN	44%	Geobacillus stearothermophilus	Crystal structure of UvrA-UvrB interaction domains
  6N9L	43%	Thermotoga maritima	Crystal structure of T. maritima UvrA d117-399 with ADP
  2VF8	42%	DEINOCOCCUS RADIODURANS	Crystal structure of UvrA2 from Deinococcus radiodurans
  2VF7	42%	DEINOCOCCUS RADIODURANS	Crystal structure of UvrA2 from Deinococcus radiodurans

• Links to additional information on uvrA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.742 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology
  • Mycobrowser
  • PATRIC

Amino Acid Sequence

VADRLIVKGAREHNLRSVDLDLPRDALIVFTGLSGSGKSSLAFDTIFAEGQRRYVESLSAYARQFLGQMDKPDVDFIEGLSPAVSIDQKSTNRNPRSTVG
TITEVYDYLRLLYARAGTPHCPTCGERVARQTPQQIVDQVLAMPEGTRFLVLAPVVRTRKGEFADLFDKLNAQGYSRVRVDGVVHPLTDPPKLKKQEKHD
IEVVVDRLTVKAAAKRRLTDSVETALNLADGIVVLEFVDHELGAPHREQRFSEKLACPNGHALAVDDLEPRSFSFNSPYGACPECSGLGIRKEVDPELVV
PDPDRTLAQGAVAPWSNGHTAEYFTRMMAGLGEALGFDVDTPWRKLPAKARKAILEGADEQVHVRYRNRYGRTRSYYADFEGVLAFLQRKMSQTESEQMK
ERYEGFMRDVPCPVCAGTRLKPEILAVTLAGESKGEHGAKSIAEVCELSIADCADFLNALTLGPREQAIAGQVLKEIRSRLGFLLDVGLEYLSLSRAAAT
LSGGEAQRIRLATQIGSGLVGVLYVLDEPSIGLHQRDNRRLIETLTRLRDLGNTLIVVEHDEDTIEHADWIVDIGPGAGEHGGRIVHSGPYDELLRNKDS
ITGAYLSGRESIEIPAIRRSVDPRRQLTVVGAREHNLRGIDVSFPLGVLTSVTGVSGSGKSTLVNDILAAVLANRLNGARQVPGRHTRVTGLDYLDKLVR
VDQSPIGRTPRSNPATYTGVFDKIRTLFAATTEAKVRGYQPGRFSFNVKGGRCEACTGDGTIKIEMNFLPDVYVPCEVCQGARYNRETLEVHYKGKTVSE
VLDMSIEEAAEFFEPIAGVHRYLRTLVDVGLGYVRLGQPAPTLSGGEAQRVKLASELQKRSTGRTVYILDEPTTGLHFDDIRKLLNVINGLVDKGNTVIV
IEHNLDVIKTSDWIIDLGPEGGAGGGTVVAQGTPEDVAAVPASYTGKFLAEVVGGGASAATSRSNRRRNVSA

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)	2.69 (0.56)	1.58 (0.81)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link