TB Genome Annotation Portal

Rv3398c (idsA1)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: geranylgeranyl diphosphate synthase type I
  • REFSEQ: multifunctional dimethylallyltransferase/farnesyl diphosphate synthetase/ farnesyltranstransferase
  • PATRIC: Dimethylallyltransferase (EC 2.5.1.1); Geranyltranstransferase (farnesyldiphosphate synthase) (EC 2.5.1.10); Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.29)
  • TUBERCULIST: Probable multifunctional geranylgeranyl pyrophosphate synthetase IdsA1 (GGPP synthetase) (ggppsase) (geranylgeranyl diphosphate synthase): dimethylallyltransferase (prenyltransferase) (geranyl-diphosphate synthase) + geranyltranstransferase (farnesyl-diphosphate synthase) (farnesyl-pyrophosphate synthetase) (farnesyl diphosphate synthetase) (FPP synthetase) + farnesyltranstransferase (geranylgeranyl-diphosphate synthase)
  • NCBI: Probable multifunctional geranylgeranyl pyrophosphate synthetase IdsA1 (GGPP synthetase) (ggppsase) (geranylgeranyl diphosphate synthase): dimethylallyltransferase (prenyltransferase) (geranyl-diphosphate synthase) + geranyltranstransferase (farnesyl-diphosphate synthase) (farnesyl-pyrophosphate synthetase) (farnesyl diphosphate synthetase) (FPP synthetase) + farnesyltranstransferase (geranylgeranyl-diphosphate synthase)
  • updated information (H37Rv4):
    • gene name: idsA1
    • function:
    • reference:
• Type: Not Target
• Start: 3815027
• End: 3816106
• Operon:


• Trans-membrane region:
  
• Role: I.G.11 - Menaquinone, PQQ, ubiquinone and other terpenoids
• GO terms:
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0045337 - farnesyl diphosphate biosynthetic process (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0033386 - geranylgeranyl diphosphate biosynthetic process (Uniprot)
  • GO:0033384 - geranyl diphosphate biosynthetic process (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016126 - sterol biosynthetic process (Uniprot)
  • GO:0008299 - isoprenoid biosynthetic process (Uniprot)
  • GO:0006629 - lipid metabolic process (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005506 - iron ion binding (Uniprot)
  • GO:0004337 - geranyltranstransferase activity (Uniprot)
  • GO:0004161 - dimethylallyltranstransferase activity (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • IPP[c] + DMPP[c] -> PPI[c] + GPP[c]
  • FPP[c] + IPP[c] -> PPI[c] + GGPP[c]
  • IPP[c] + GGPP[c] -> PPI[c] + PPPP[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):
  

  PDB	aa ident	species	PDB title
  3NF2	50%	Streptomyces coelicolor	Crystal structure of polyprenyl synthetase from Streptomyces coelicolor A3(2)
  3M0G	40%	Rhodobacter capsulatus	CRYSTAL STRUCTURE OF putative farnesyl diphosphate synthase from Rhodobacter capsulatus
  3LVS	40%	Rhodobacter capsulatus	Crystal structure of farnesyl diphosphate synthase from rhodobacter capsulatus sb1003
  5XN6	40%	Oryza sativa Japonica Group	Heterodimer crystal structure of geranylgeranyl diphosphate synthases 1 with GGPPS Recruiting Protein(OsGRP) from Oryza sativa
  5XN5	40%	Oryza sativa Japonica Group	Homo-dimer crystal structure of geranylgeranyl diphosphate synthases 1 from Oryza sativa
  5E8L	39%	Arabidopsis thaliana	Crystal structure of geranylgeranyl pyrophosphate synthase 11 from Arabidopsis thaliana
  4LLT	39%	Roseobacter denitrificans	Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site
  4LLS	39%	Roseobacter denitrificans	Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with IPP, GSPP, and calcium bound in active site
  2J1P	39%	SINAPIS ALBA	Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP
  3P41	38%	Pseudomonas fluorescens	Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate

• Links to additional information on idsA1:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.966 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MRGTDEKYGLPPQPDSDRMTRRTLPVLGLAHELITPTLRQMADRLDPHMRPVVSYHLGWSDERGRPVNNNCGKAIRPALVFVAAEAAGADPHSAIPGAVS
VELVHNFSLVHDDLMDRDEHRRHRPTVWALWGDAMALLAGDAMLSLAHEVLLDCDSPHVGAALRAISEATRELIRGQAADTAFESRTDVALDECLKMAEG
KTAALMAASAEVGALLAGAPRSVREALVAYGRHIGLAFQLVDDLLGIWGRPEITGKPVYSDLRSRKKTLPVTWTVAHGGSAGRRLAAWLVDETGSQTASD
DELAAVAELIECGGGRRWASAEARRHVTQGIDMVARIGIPDRPAAELQDLAHYIVDRQA

Additional Information