TB Genome Annotation Portal

Rv3582c (ispD)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
  • REFSEQ: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
  • PATRIC: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC 2.7.7.60)
  • TUBERCULIST: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (MEP cytidylyltransferase) (MCT)
  • NCBI: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase IspD (MEP cytidylyltransferase) (MCT)
  • updated information (H37Rv4):
    • gene name: ispD
    • function:
    • reference:
• Type: Essential
• Start: 4024344
• End: 4025039
• Operon:


• Trans-membrane region:
  
• Role: V - Conserved hypotheticals
• GO terms:
  • GO:0070567 - cytidylyltransferase activity (Uniprot)
  • GO:0051484 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process (Uniprot)
  • GO:0050518 - 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0030145 - manganese ion binding (Uniprot)
  • GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway (Uniprot)
  • GO:0016779 - nucleotidyltransferase activity (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0008299 - isoprenoid biosynthetic process (Uniprot)
  • GO:0008270 - zinc ion binding (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
  • GO:0002135 - CTP binding (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • CTP[c] + MDE4P[c] -> PPI[c] + CDPMDE[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: 3okr, 2xwn, 3q7u, 3q80
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3Q80	100%	Mycobacterium tuberculosis	Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) Complexed with CDP-ME
  3Q7U	100%	Mycobacterium tuberculosis	Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) complexed with CTP
  3OKR	99%	Mycobacterium tuberculosis	Structure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD)
  2XWN	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of IspD from Mycobacterium tuberculosis in complex with CTP and Mg
  2XWM	62%	MYCOBACTERIUM SMEGMATIS	Crystal structure of IspD from Mycobacterium smegmatis in complex with CMP
  2XWL	62%	MYCOBACTERIUM SMEGMATIS	Crystal structure of IspD from Mycobacterium smegmatis in complex with CTP and Mg
  2PX7	41%	Thermus thermophilus HB8	Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8
  4ZDQ	36%	Burkholderia thailandensis	Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
  4YS8	36%	Burkholderia thailandensis	Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis

• Links to additional information on ispD:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -2.267 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VVREAGEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEP
EFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHI
GGQVQVVDGDPLAFKITTKLDLLLAQAIVRG

Additional Information