TB Genome Annotation Portal

Rv1011 (ispE)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
  • REFSEQ: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
  • PATRIC: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC 2.7.1.148)
  • TUBERCULIST: Probable 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase IspE (CMK) (4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase)
  • NCBI: Probable 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase IspE (CMK) (4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase)
  • updated information (H37Rv4):
    • gene name: ispE
    • function:
    • reference:
• Type: Not Target
• Start: 1130191
• End: 1131111
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0050515 - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016310 - phosphorylation (Uniprot)
  • GO:0016301 - kinase activity (Uniprot)
  • GO:0016114 - terpenoid biosynthetic process (Uniprot)
  • GO:0008299 - isoprenoid biosynthetic process (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0000166 - nucleotide binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • ATP[c] + CDPMDE[c] -> ADP[c] + 2PCDPMDE[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: 3pye, 3pyd, 3pyg, 3pyf
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3PYG	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in complex with ADP
  3PYF	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in complex with AMP-PNP
  3PYE	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in complex with CDPME
  3PYD	100%	Mycobacterium tuberculosis	crystal structure of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis
  4EMD	78%	Mycobacterium abscessus	Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to CMP and SO4
  4ED4	78%	Mycobacterium abscessus	Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abcessus, bound to ATP
  4DXL	78%	Mycobacterium abscessus	Crystal structure of IspE (4-diphosphocytidyl-2-C-methyl-D-erythritol kinase) from Mycobacterium abscessus, bound to CMP and ATP
  1UEK	39%	Thermus thermophilus	Crystal structure of 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase
  2WW4	37%	ESCHERICHIA COLI	a triclinic crystal form of E. coli 4-diphosphocytidyl-2C-methyl-D- erythritol kinase
  1OJ4	37%	ESCHERICHIA COLI	Ternary complex of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

• Links to additional information on ispE:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -6.247 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VPTGSVTVRVPGKVNLYLAVGDRREDGYHELTTVFHAVSLVDEVTVRNADVLSLELVGEGADQLPTDERNLAWQAAELMAEHVGRAPDVSIMIDKSIPVA
GGMAGGSADAAAVLVAMNSLWELNVPRRDLRMLAARLGSDVPFALHGGTALGTGRGEELATVLSRNTFHWVLAFADSGLLTSAVYNELDRLREVGDPPRL
GEPGPVLAALAAGDPDQLAPLLGNEMQAAAVSLDPALARALRAGVEAGALAGIVSGSGPTCAFLCTSASSAIDVGAQLSGAGVCRTVRVATGPVPGARVV
SAPTEV

Additional Information