TB Genome Annotation Portal

Rv2361c (-)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: undecaprenyl pyrophosphate synthase
  • REFSEQ: long (C50) chain Z-isoprenyl diphosphate synthase (Z-decaprenyl diphosphate synthase)
  • PATRIC: Decaprenyl diphosphate synthase (EC 2.5.1.91)
  • TUBERCULIST: Long (C50) chain Z-isoprenyl diphosphate synthase (Z-decaprenyl diphosphate synthase)
  • NCBI: Long (C50) chain Z-isoprenyl diphosphate synthase (Z-decaprenyl diphosphate synthase)
  • updated information (H37Rv4):
    • gene name: uppS
    • function: decaprenyl diphosphate synthase
    • reference: Wang 2008, PMID: 18597781
• Type: Essential
• Start: 2642578
• End: 2643468
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0050347 - trans-octaprenyltranstransferase activity (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0033850 - Z-farnesyl diphosphate synthase activity (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016094 - polyprenol biosynthetic process (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0008834 - di-trans,poly-cis-decaprenylcistransferase activity (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0002094 - polyprenyltransferase activity (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • FPP[c] + 7 IPP[c] -> DPP[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: 2vg4, 2vg2, 2vg3
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  4ONC	100%	Mycobacterium tuberculosis	Crystal Structure of Mycobacterium Tuberculosis Decaprenyl Diphosphate Synthase in Complex with BPH-640
  2VG4	100%	MYCOBACTERIUM TUBERCULOSIS	Rv2361 native
  2VG3	100%	MYCOBACTERIUM TUBERCULOSIS	Rv2361 with citronellyl pyrophosphate
  2VG2	100%	MYCOBACTERIUM TUBERCULOSIS	Rv2361 with IPP
  6IME	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Rv2361c complex with substrate analogues
  7CPN	65%	Thermobifida fusca (strain YX)	CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA
  7CPM	65%	Thermobifida fusca (strain YX)	CRYSTAL STRUCTURE OF DODECAPRENYL DIPHOSPHATE SYNTHASE FROM THERMOBIFIDA FUSCA
  6LOI	43%	Enterococcus faecalis	Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosphate synthase(EfaUPPS)
  5KH5	41%	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS) IN COMPLEX WITH ~{N}-(3-azanyl-3-oxidanylidene-propyl)-5-(1-benzothiophen-5-yl)-1-(phenylmethyl)-~{N}-[(4-propan-2-yloxyphenyl)methyl]pyrazole-4-carboxamide
  5KH4	41%	Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)	Crystal Structure of Steptococcus pneumoniae Undecaprenyl pyrophosphate Synthase (UPPS) with FARNESYL DIPHOSPHATE

• Links to additional information on Rv2361c:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -10.993 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VARDARKRTSSNFPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVV
IDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVRRRRDTLKKLGVRIRWVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTE
ITEATREIAREVAAGRLNPERITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYASRTRRFGSA

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)	1.36 (0.09)	0.7 (0.17)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link