TB Genome Annotation Portal

Rv0217c (lipW)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: esterase/lipase
  • REFSEQ: esterase LipW
  • PATRIC: Esterase LipW
  • TUBERCULIST: Possible esterase LipW
  • NCBI: Possible esterase LipW
  • updated information (H37Rv4):
    • gene name: lipW
    • function:
    • reference:
• Type: Not Target
• Start: 259923
• End: 260831
• Operon:


• Trans-membrane region:
  
• Role: II.B.5 - Esterases and lipases
• GO terms:
  • GO:0034338 - short-chain carboxylesterase activity (Uniprot)
  • GO:0016787 - hydrolase activity (Uniprot)
  • GO:0009056 - catabolic process (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • PHOSPHATIDYLCHOLINE[c] -> DAG[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
  3QH4	43%	Mycobacterium marinum	Crystal structure of esterase LipW from Mycobacterium marinum
  1U4N	42%	Alicyclobacillus acidocaldarius	Crystal Structure Analysis of the M211S/R215L EST2 mutant
  1QZ3	42%	Alicyclobacillus acidocaldarius	CRYSTAL STRUCTURE OF MUTANT M211S/R215L OF CARBOXYLESTERASE EST2 COMPLEXED WITH HEXADECANESULFONATE
  1EVQ	42%	Alicyclobacillus acidocaldarius	THE CRYSTAL STRUCTURE OF THE THERMOPHILIC CARBOXYLESTERASE EST2 FROM ALICYCLOBACILLUS ACIDOCALDARIUS
  6K34	41%	Mycobacterium sp. YC-RL4	Crystal Structure of DphMB1
  2HM7	41%	Alicyclobacillus acidocaldarius	Crystal Structure Analysis of the G84S EST2 mutant
  1LZL	40%	Rhodococcus sp.	Bacterial Heroin Esterase
  1LZK	40%	Rhodococcus sp.	BACTERIAL HEROIN ESTERASE COMPLEX WITH TRANSITION STATE ANALOG DIMETHYLARSENIC ACID
  6AAE	39%	uncultured bacterium	Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136
  6IEY	39%	uncultured bacterium	Crystal structure of Chloramphenicol-Metabolizaing Enzyme EstDL136-Chloramphenicol complex

• Links to additional information on lipW:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.927 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VSGNEVHPDLRRIAVVTPRQLVGPRTLPVMRALIVVAGLRMSRTPPDIEVLTLESGVGVRLYRPAGSNEPAPALLWIHAGGYVMGTAQQDDRLCLRFSSR
LGITVASVDYRLAPENPYPAALGDCYSALTWLASLPAVDPARVAIGGASAGGGLAAALALLARDRGGITPAFQLLVYPMLDDRPSIAPANPHYRLWNGRA
NRFGWRAYLGDADARVAVPGRRDDLGGLAPAWIGVGTHDLLHDEDLAYAERLTAAGVPCQVEVVEGAFHGFDRVAPNVGVSQRFFTSQCNSLRAALALSN
RT

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	YES
omega peak height (95%CI lower bound)	1.55 (0.35)	2.08 (1.13)
codons under selection		214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 234, 235, 236, 237, 238, 239
omega plots
genetic variants*	link	link
statistics at each codon	link	link