TB Genome Annotation Portal

Rv1916 (aceAb)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: isocitrate lyase
  • REFSEQ: isocitrate lyase
  • PATRIC: Isocitrate lyase (EC 4.1.3.1) group III Mycobacterial type ICL2
  • TUBERCULIST: Probable isocitrate lyase AceAb [second part] (isocitrase) (isocitratase) (Icl)
  • NCBI: Probable isocitrate lyase AceAb [second part] (isocitrase) (isocitratase) (Icl)
  • updated information (H37Rv4):
    • gene name: aceAb
    • function:
    • reference:
• Type: Not Target
• Start: 2161566
• End: 2162762
• Operon:


• Trans-membrane region:
  
• Role: I.B.4 - Glyoxylate bypass
• GO terms:
  • GO:0019752 - carboxylic acid metabolic process (Uniprot)
  • GO:0016829 - lyase activity (Uniprot)
  • GO:0004451 - isocitrate lyase activity (Uniprot)
  • GO:0003824 - catalytic activity (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
  6EE1	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA
  6EDZ	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis ICL2 in complex with acetyl-CoA, form I
  6EDW	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of Mycobacterium tuberculosis ICL2 in the apo form
  3LG3	48%	Yersinia pestis	1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92
  6XPP	47%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of itaconate modified Mycobaterium tuberculosis isocitrate lyase
  6C4C	47%	Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman)	Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate
  6C4A	47%	Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman)	Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with pyruvate
  5DQL	47%	Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman)	Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis
  1F8M	47%	Mycobacterium tuberculosis H37Rv	CRYSTAL STRUCTURE OF 3-BROMOPYRUVATE MODIFIED ISOCITRATE LYASE (ICL) FROM MYCOBACTERIUM TUBERCULOSIS
  1F8I	47%	Mycobacterium tuberculosis H37Rv	CRYSTAL STRUCTURE OF ISOCITRATE LYASE:NITROPROPIONATE:GLYOXYLATE COMPLEX FROM MYCOBACTERIUM TUBERCULOSIS

• Links to additional information on aceAb:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.334 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTYGEAVADVLEFGQSEGEPIGMAPEEWRAFAARASLHAARAKAKELGADPPWDCELAKTPEGYYQIRGGIPYAIAKSLAAAPFADILWMETKTADLADA
RQFAEAIHAEFPDQMLAYNLSPSFNWDTTGMTDEEMRRFPEELGKMGFVFNFITYGGHQIDGVAAEEFATALRQDGMLALARLQRKMRLVESPYRTPQTL
VGGPRSDAALAASSGRTATTKAMGKGSTQHQHLVQTEVPRKLLEEWLAMWSGHYQLKDKLRVQLRPQRAGSEVLELGIHGESDDKLANVIFQPIQDRRGR
TILLVRDQNTFGAELRQKRLMTLIHLWLVHRFKAQAVHYVTPTDDNLYQTSKMKSHGIFTEVNQEVGEIIVAEVNHPRIAELLTPDRVALRKLITKEA

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)	1.82 (0.4)	1.73 (0.91)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link