TB Genome Annotation Portal

Rv1131 (prpC)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: citrate synthase
  • REFSEQ: citrate synthase
  • PATRIC: 2-methylcitrate synthase (EC 2.3.3.5)
  • TUBERCULIST: Probable methylcitrate synthase PrpC
  • NCBI: Probable methylcitrate synthase PrpC
  • updated information (H37Rv4):
    • gene name: prpC
    • function:
    • reference:
• Type: Not Target
• Start: 1256132
• End: 1257313
• Operon:


• Trans-membrane region:
  
• Role: I.B.3 - TCA cycle
• GO terms:
  • GO:0050440 - 2-methylcitrate synthase activity (Uniprot)
  • GO:0046912 - transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer (Uniprot)
  • GO:0036440 - citrate synthase activity (Uniprot)
  • GO:0019679 - propionate metabolic process, methylcitrate cycle (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0006099 - tricarboxylic acid cycle (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • OA[c] + PROPIONYLCOA[c] -> COA[c] + 2METHYLCITRATE[c]
  • ACCOA[c] + OA[c] -> COA[c] + CIT[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: 3hwk
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3HWK	100%	Mycobacterium tuberculosis	Crystal structure of methylcitrate synthase from Mycobacterium tuberculosis
  1A59	58%	Antarctic bacterium DS2-3R	COLD-ACTIVE CITRATE SYNTHASE
  1IXE	41%	Thermus thermophilus	Crystal structure of citrate synthase from Thermus thermophilus HB8
  1IOM	41%	Thermus thermophilus	CRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM THERMUS THERMOPHILUS HB8
  3TQG	41%	Coxiella burnetii	Structure of the 2-methylcitrate synthase (prpC) from Coxiella burnetii
  6S87	41%	Pseudomonas aeruginosa PAO1	Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in complex with oxaloacetate.
  6S6F	41%	Pseudomonas aeruginosa PAO1	Crystal structure of 2-methylcitrate synthase (PrpC) from Pseudomonas aeruginosa in apo form.
  1AJ8	40%	Pyrococcus furiosus	CITRATE SYNTHASE FROM PYROCOCCUS FURIOSUS
  2P2W	39%	Thermotoga maritima	Crystal structure of citrate synthase from Thermotoga maritima MSB8
  2C6X	38%	BACILLUS SUBTILIS	Structure of Bacillus subtilis citrate synthase

• Links to additional information on prpC:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.501 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTGPLAAARSVAATKSMTAPTVDERPDIKKGLAGVVVDTTAISKVVPQTNSLTYRGYPVQDLAARCSFEQVAFLLWRGELPTDAELALFSQRERASRRVD
RSMLSLLAKLPDNCHPMDVVRTAISYLGAEDPDEDDAAANRAKAMRMMAVLPTIVAIDMRRRRGLPPIAPHSGLGYAQNFLHMCFGEVPETAVVSAFEQS
MILYAEHGFNASTFAARVVTSTQSDIYSAVTGAIGALKGRLHGGANEAVMHDMIEIGDPANAREWLRAKLARKEKIMGFGHRVYRHGDSRVPTMKRALER
VGTVRDGQRWLDIYQVLAAEMASATGILPNLDFPTGPAYYLMGFDIASFTPIFVMSRITGWTAHIMEQATANALIRPLSAYCGHEQRVLPGTF

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)	1.5 (0.17)	0.5 (0.16)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link