TB Genome Annotation Portal

Rv3148 (nuoD)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: NADH-quinone oxidoreductase subunit D
  • REFSEQ: NADH dehydrogenase subunit D
  • PATRIC: NADH-ubiquinone oxidoreductase chain D (EC 1.6.5.3)
  • TUBERCULIST: Probable NADH dehydrogenase I (chain D) NuoD (NADH-ubiquinone oxidoreductase chain D)
  • NCBI: Probable NADH dehydrogenase I (chain D) NuoD (NADH-ubiquinone oxidoreductase chain D)
  • updated information (H37Rv4):
    • gene name: nuoD
    • function:
    • reference:
• Type: Not Target
• Start: 3513338
• End: 3514660
• Operon:


• Trans-membrane region:
  
• Role: I.B.6.a - aerobic
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0051287 - NAD binding (Uniprot)
  • GO:0048038 - quinone binding (Uniprot)
  • GO:0016651 - oxidoreductase activity, acting on NAD(P)H (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • MK[c] + NADH[c] -> 4 H[c] + MKH2[c] + NAD[c]
• 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
  6ZJY	47%	Thermus thermophilus	Respiratory complex I from Thermus thermophilus, NAD+ dataset, minor state
  6ZJN	47%	Thermus thermophilus	Respiratory complex I from Thermus thermophilus, NADH dataset, minor state
  6ZJL	47%	Thermus thermophilus	Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state
  6ZIY	47%	Thermus thermophilus	Respiratory complex I from Thermus thermophilus, NADH dataset, major state
  6Y11	47%	Thermus thermophilus	Respiratory complex I from Thermus thermophilus
  6Q8X	47%	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Respiratory complex I from Thermus thermophilus with bound Pyridaben.
  6Q8W	47%	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Respiratory complex I from Thermus thermophilus with bound Aureothin.
  6Q8O	47%	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)	Respiratory complex I from Thermus thermophilus with bound Piericidin A
  6I1P	47%	Thermus thermophilus HB8	Respiratory complex I from Thermus thermophilus with bound NADH
  6I0D	47%	Thermus thermophilus HB8	Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone

• Links to additional information on nuoD:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.643 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTAIADSAGGAGETVLVAGGQDWQQVVDAARSADPGERIVVNMGPQHPSTHGVLRLILEIEGETVVEARCGIGYLHTGIEKNLEYRYWTQGVTFVTRMDY
LSPFFNETAYCLGVEKLLGITDEIPERVNVIRVLMMELNRISSHLVALATGGMELGAMTPMFVGFRAREIVLTLFEKITGLRMNSAYIRPGGVAQDLPPN
AATEIAEALKQLRQPLREMGELLNENAIWKARTQGVGYLDLTGCMALGITGPILRSTGLPHDLRKSEPYCGYQHYEFDVITDDSCDAYGRYMIRVKEMWE
SMKIVEQCLDKLRPGPTMISDRKLAWPADLQVGPDGLGNSPKHIAKIMGSSMEALIHHFKLVTEGIRVPAGQVYVAVESPRGELGVHMVSDGGTRPYRVH
YRDPSFTNLQSVAAMCEGGMVADLIAAVASIDPVMGGVDR

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)	1.56 (0.18)	1.3 (0.49)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link