TB Genome Annotation Portal

Rv0542c (menE)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: O-succinylbenzoic acid-CoA ligase
  • REFSEQ: O-succinylbenzoic acid--CoA ligase
  • PATRIC: O-succinylbenzoic acid--CoA ligase (EC 6.2.1.26)
  • TUBERCULIST: Possible O-succinylbenzoic acid--CoA ligase MenE (OSB-CoA synthetase) (O-succinylbenzoate-CoA synthase)
  • NCBI: Possible O-succinylbenzoic acid--CoA ligase MenE (OSB-CoA synthetase) (O-succinylbenzoate-CoA synthase)
  • updated information (H37Rv4):
    • gene name: menE
    • function:
    • reference:
• Type: Not Target
• Start: 634416
• End: 635504
• Operon:


• Trans-membrane region:
  
• Role: I.G.11 - Menaquinone, PQQ, ubiquinone and other terpenoids
• GO terms:
  • GO:0040007 - growth (Uniprot)
  • GO:0016874 - ligase activity (Uniprot)
  • GO:0009234 - menaquinone biosynthetic process (Uniprot)
  • GO:0008756 - o-succinylbenzoate-CoA ligase activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0000166 - nucleotide binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • ATP[c] + COA[c] + OSB[c] -> PPI[c] + AMP[c] + OSBCOA[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
  6E97	37%	Thermobifida fusca	Crystal structure of the aryl acid adenylating enzyme FscC from Fuscachelin NRPS in complex with DHB-adenylate
  6E8O	37%	Thermobifida fusca	Crystal structure of aryl acid adenylating enzyme FscC from Fuscachelin NRPS in complex with AMP

• Links to additional information on menE:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -6.088 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VLGGSDPALVAVPTQHESLLGALRVGEQIDDDVALVVTTSGTTGPPKGAMLTAAALTASASAAHDRLGGPGSWLLAVPPYHIAGLAVLVRSVIAGSVPVE
LNVSAGFDVTELPNAIKRLGSGRRYTSLVAAQLAKALTDPAATAALAELDAVLIGGGPAPRPILDAAAAAGITVVRTYGMSETSGGCVYDGVPLDGVRLR
VLAGGRIAIGGATLAKGYRNPVSPDPFAEPGWFHTDDLGALESGDSGVLTVLGRADEAISTGGFTVLPQPVEAALGTHPAVRDCAVFGLADDRLGQRVVA
AIVVGDGCPPPTLEALRAHVARTLDVTAAPRELHVVNVLPRRGIGKVDRAALVRRFAGEADQ

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)	1.72 (0.36)	0.75 (0.24)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link