TB Genome Annotation Portal

Rv0066c (icd2)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: isocitrate dehydrogenase NADP-dependent
  • REFSEQ: isocitrate dehydrogenase
  • PATRIC: Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)
  • TUBERCULIST: Probable isocitrate dehydrogenase [NADP] Icd2 (oxalosuccinate decarboxylase) (IDH) (NADP+-specific ICDH) (IDP)
  • NCBI: Probable isocitrate dehydrogenase [NADP] Icd2 (oxalosuccinate decarboxylase) (IDH) (NADP+-specific ICDH) (IDP)
  • updated information (H37Rv4):
    • gene name: icd2
    • function:
    • reference:
• Type: Not Target
• Start: 72274
• End: 74511
• Operon:


• Trans-membrane region:
  
• Role: I.B.3 - TCA cycle
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0042803 - protein homodimerization activity (Uniprot)
  • GO:0006102 - isocitrate metabolic process (Uniprot)
  • GO:0006099 - tricarboxylic acid cycle (Uniprot)
  • GO:0006097 - glyoxylate cycle (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005576 - extracellular region (Uniprot)
  • GO:0004450 - isocitrate dehydrogenase (NADP+) activity (Uniprot)
  • GO:0004448 - isocitrate dehydrogenase activity (Uniprot)
  • GO:0000287 - magnesium ion binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • NADP[c] + ICIT[c] -> NADPH[c] + CO2[c] + AKG[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
  5KVU	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from Mycobacterium tuberculosis
  4ZDA	81%	Mycobacterium smegmatis	Crystal structure of isocitrate dehydrogenase in complex with isocitrate and Mn from M. smegmatis
  5Z16	76%	Acinetobacter baumannii	A novel dimeric isocitrate dehydrogenase from Acinetobacter baumannii
  6G3U	67%	Pseudomonas aeruginosa	Structure of Pseudomonas aeruginosa Isocitrate Dehydrogenase, IDH
  1J1W	61%	Azotobacter vinelandii	Crystal Structure Of The Monomeric Isocitrate Dehydrogenase In Complex With NADP+
  1ITW	61%	Azotobacter vinelandii	Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn
  3MBC	57%	Corynebacterium glutamicum	Crystal structure of monomeric isocitrate dehydrogenase from Corynebacterium glutamicum in complex with NADP
  2B0T	57%	Corynebacterium glutamicum	Structure of Monomeric NADP Isocitrate dehydrogenase

• Links to additional information on icd2:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.403 (from Jeremy Rock's lab)
  • Photo of spot titer

Amino Acid Sequence

MSAEQPTIIYTLTDEAPLLATYAFLPIVRAFAEPAGIKIEASDISVAARILAEFPDYLTEEQRVPDNLAELGRLTQLPDTNIIKLPNISASVPQLVAAIK
ELQDKGYAVPDYPADPKTDQEKAIKERYARCLGSAVNPVLRQGNSDRRAPKAVKEYARKHPHSMGEWSMASRTHVAHMRHGDFYAGEKSMTLDRARNVRM
ELLAKSGKTIVLKPEVPLDDGDVIDSMFMSKKALCDFYEEQMQDAFETGVMFSLHVKATMMKVSHPIVFGHAVRIFYKDAFAKHQELFDDLGVNVNNGLS
DLYSKIESLPASQRDEIIEDLHRCHEHRPELAMVDSARGISNFHSPSDVIVDASMPAMIRAGGKMYGADGKLKDTKAVNPESTFSRIYQEIINFCKTNGQ
FDPTTMGTVPNVGLMAQQAEEYGSHDKTFEIPEDGVANIVDVATGEVLLTENVEAGDIWRMCIVKDAPIRDWVKLAVTRARISGMPVLFWLDPYRPHENE
LIKKVKTYLKDHDTEGLDIQIMSQVRSMRYTCERLVRGLDTIAATGNILRDYLTDLFPILELGTSAKMLSVVPLMAGGGMYETGAGGSAPKHVKQLVEEN
HLRWDSLGEFLALGAGFEDIGIKTGNERAKLLGKTLDAAIGKLLDNDKSPSRKTGELDNRGSQFYLAMYWAQELAAQTDDQQLAEHFASLADVLTKNEDV
IVRELTEVQGEPVDIGGYYAPDSDMTTAVMRPSKTFNAALEAVQG

Additional Information