TB Genome Annotation Portal

Rv2498c (citE)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: citrate lyase subunit beta-like protein
  • REFSEQ: citrate (Pro-3S)-lyase beta subunit
  • PATRIC: Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
  • TUBERCULIST: Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase)
  • NCBI: Probable citrate (pro-3S)-lyase (beta subunit) CitE (citrase) (citratase) (citritase) (citridesmolase) (citrase aldolase)
  • updated information (H37Rv4):
    • gene name: citE
    • function:
    • reference:
• Type: Conditional
• Start: 2812355
• End: 2813176
• Operon:


• Trans-membrane region:
  
• Role: I.B.3 - TCA cycle
• GO terms:
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0016829 - lyase activity (Uniprot)
  • GO:0006107 - oxaloacetate metabolic process (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0000287 - magnesium ion 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: 1u5v, 1u5h, 1z6k
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  6CJ4	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND ACETOACETATE
  6CJ3	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND PYRUVATE
  6CHU	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND ACETATE
  6AS5	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, ACETOACETATE AND COENZYME A
  6ARB	100%	Mycobacterium tuberculosis CDC1551	CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND COENZYME A
  6AQ4	100%	Mycobacterium tuberculosis	CRYSTAL STRUCTURE OF PROTEIN CiTE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND CITRAMALYL-COA
  1Z6K	100%	Mycobacterium tuberculosis	Citrate lyase beta subunit complexed with oxaloacetate and magnesium from M. tuberculosis
  1U5H	98%	Mycobacterium tuberculosis	Structure of Citrate Lyase beta subunit from Mycobacterium tuberculosis
  1U5V	97%	Mycobacterium tuberculosis	Structure of CitE complexed with triphosphate group of ATP form Mycobacterium tuberculosis
  3QLL	36%	Yersinia pestis	Crystal Structure of RipC from Yersinia pestis

• Links to additional information on citE:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.745 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVI
ELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAA
VGFDVTVCIHPSQIPVVRKAYRPSHEKLAWARRVLAASRSERGAFAFEGQMVDSPVLTHAETMLRRAGEATSE

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)	1.38 (0.24)	1.07 (0.49)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link