TB Genome Annotation Portal

Rv1130 (prpD)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 2-methylcitrate dehydratase
  • REFSEQ: hypothetical protein
  • PATRIC: 2-methylcitrate dehydratase (EC 4.2.1.79)
  • TUBERCULIST: Possible methylcitrate dehydratase PrpD
  • NCBI: Possible methylcitrate dehydratase PrpD
  • updated information (H37Rv4):
    • gene name: prpD
    • function:
    • reference:
• Type: Conditional
• Start: 1254555
• End: 1256135
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0047547 - 2-methylcitrate dehydratase activity (Uniprot)
  • GO:0019679 - propionate metabolic process, methylcitrate cycle (Uniprot)
  • GO:0019629 - propionate catabolic process, 2-methylcitrate cycle (Uniprot)
  • GO:0016829 - lyase activity (Uniprot)
  • GO:0010447 - response to acidic pH (Uniprot)
  • GO:0008203 - cholesterol metabolic process (Uniprot)
  • GO:0008202 - steroid metabolic process (Uniprot)
  • GO:0006629 - lipid metabolic process (Uniprot)
  • GO:0006099 - tricarboxylic acid cycle (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0003994 - aconitate hydratase activity (Uniprot)
  • GO:0047547 - 2-methylcitrate dehydratase activity (FLUTE) (FLUTE Assigned!Y1 report, ABMP data)
• Reaction(s) (based on iSM810 metabolic model):
  • 2METHYLCITRATE[c] -> 2METHYLCISACONITATE[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): (none with >35% aa id)
• Links to additional information on prpD:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.032 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • Metabolomics Workbench

Amino Acid Sequence

VPDQDTKVRFFRVFCWCPVLRMVRIMLMHAVRAWRSADDFPCTEHMAYKIAQVAADPVDVDPEVADMVCNRIIDNAAVSAASMVRRPVTVARHQALAHPV
RHGAKVFGVEGSYSADWAAWANGVAARELDFHDTFLAADYSHPADNIPPLVAVAQQLGVCGAELIRGLVTAYEIHIDLTRGICLHEHKIDHVAHLGPAVA
AGIGTMLRLDQETIYHAIGQALHLTTSTRQSRKGAISSWKAFAPAHAGKVGIEAVDRAMRGEGSPAPIWEGEDGVIAWLLAGPEHTYRVPLPAPGEPKRA
ILDSYTKQHSAEYQSQAPIDLACRLRERIGDLDQIASIVLHTSHHTHVVIGTGSGDPQKFDPDASRETLDHSLPYIFAVALQDGCWHHERSYAPERARRS
DTVALWHKISTVEDPEWTRRYHCADPAKKAFGARAEVTLHSGEVIVDELAVADAHPLGTRPFERKQYVEKFTELADGVVEPVEQQRFLAVVESLADLESG
AVGGLNVLVDPRVLDKAPVIPPGIFR

(Nucleotide sequence available on KEGG)

Additional Information

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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?	YES	YES
omega peak height (95%CI lower bound)	3.5 (1.48)	4.07 (2.45)
codons under selection	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

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