TB Genome Annotation Portal

Rv3581c (ispF)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 2-C-methyl-D-erythritol 24-cyclodiphosphate synthase
  • REFSEQ: 2-C-methyl-D-erythritol 24-cyclodiphosphate synthase
  • PATRIC: 2-C-methyl-D-erythritol 24-cyclodiphosphate synthase (EC 4.6.1.12)
  • TUBERCULIST: Probable 2C-methyl-D-erythritol 24-cyclodiphosphate synthase IspF (MECPS)
  • NCBI: Probable 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (MECPS)
  • updated information (H37Rv4):
    • gene name: ispF
    • function:
    • reference:
• Type: Essential
• Start: 4023868
• End: 4024347
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0051483 - terpenoid biosynthetic process, mevalonate-independent (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (Uniprot)
  • GO:0016829 - lyase activity (Uniprot)
  • GO:0016114 - terpenoid biosynthetic process (Uniprot)
  • GO:0008685 - 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity (Uniprot)
  • GO:0008299 - isoprenoid biosynthetic process (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • 2PCDPMDE[c] -> CMP[c] + MDECPP[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
  2UZH	75%	MYCOBACTERIUM SMEGMATIS	Mycobacterium smegmatis 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (IspF)
  1IV1	45%	Thermus thermophilus	Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase
  1IV4	45%	Thermus thermophilus	Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)
  1IV3	45%	Thermus thermophilus	Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms)
  1IV2	45%	Thermus thermophilus	Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form CDP)
  1T0A	41%	Shewanella oneidensis	Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis
  2PMP	41%	Arabidopsis thaliana	Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana
  3T80	41%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine
  3GHZ	41%	Salmonella typhimurium	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium
  3FBA	41%	Escherichia coli	Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

• Links to additional information on ispF:
  • KEGG - nucleotide and amino acid sequences of gene
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -7.073 (from Jeremy Rock's lab)
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VNQLPRVGLGTDVHPIEPGRPCWLVGLLFPSADGCAGHSDGDVAVHALCDAVLSAAGLGDIGEVFGVDDPRWQGVSGADMLRHVVVLITQHGYRVGNAVV
QVIGNRPKIGWRRLEAQAVLSRLLNAPVSVSATTTDGLGLTGRGEGLAAIATALVVSLR

Additional Information