TB Genome Annotation Portal

Rv2502c (accD1)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: 3-methylcrotonyl-CoA carboxylase beta subunit
  • REFSEQ: acetyl-/propionyl-CoA carboxylase subunit beta
  • PATRIC: Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)
  • TUBERCULIST: Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1
  • NCBI: Probable acetyl-/propionyl-CoA carboxylase (beta subunit) AccD1
  • updated information (H37Rv4):
    • gene name: accD1
    • function:
    • reference:
• Coordinates in H37Rv: 2816885 - 2818474
• Gene length: 1590 bp (with stop codon), 529 aa (without stop codon)
• Operon:


• Trans-membrane region:
  
• Role: I.A.3 - Fatty acids
• GO terms:
  • GO:0016874 - ligase activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • PROPIONYLCOA[c] + BIOTIN_CO2[c] -> SMMALONYLCOA[c] + 0.999 BIOTIN[c]
  • BIOTIN_CO2[c] + 3MBECOA[c] -> 0.999 BIOTIN[c] + MGLUTCOA[c]
  • ACCOA[c] + BIOTIN_CO2[c] -> 0.999 BIOTIN[c] + MALCOA[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 Latest Homologs in PDB
• Top 10 Homologs in PDB (as of Apr 2026):
  

  PDB	aa ident	species	PDB title
  4Q0G	99%	Mycobacterium tuberculosis	Crystal structure of beta subunit of acyl-CoA carboxylase AccD1 from Mycobacterium tuberculosis
  9YX0	84%	Mycolicibacterium smegmatis MC2 155	Structure of the 3-methylcrotonyl-coenzyme A carboxylase from Mycobacterium smegmatis
  3U9T	69%	Pseudomonas aeruginosa	Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC) 750 kD holoenzyme, free enzyme
  3U9S	69%	Pseudomonas aeruginosa	Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC) 750 kD holoenzyme, CoA complex
  3U9R	69%	Pseudomonas aeruginosa	Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC), beta subunit
  8XL8	65%	Homo sapiens	Structure of human 3-methylcrotonyl-CoA carboxylase in complex with propionyl-CoA (MCC-PCO)
  8XL7	65%	Homo sapiens	Structure of human 3-methylcrotonyl-CoA carboxylase in complex with acetyl-CoA (MCC-ACO)
  8XL6	65%	Homo sapiens	Structure of human 3-methylcrotonyl-CoA carboxylase at apo-state (MCC-Apo)
  8K2V	65%	Homo sapiens	3-Methylcrotonyl-CoA Carboxylase in MCCD state with Acetyl CoA
  8JXN	65%	Homo sapiens	Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state with MCoA

• Links to additional information on accD1:
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 1.021 (from Jeremy Rock's lab)
  • BioCyc
  • Systems Biology

Amino Acid Sequence

VTTPSIAIAPSFADEHRRLVAELNNKLAAAALGGNERARKRHVSRGKLLPRERVDRLLDPGSPFLELAPLAAGGMYGDESPGAGIITGIGRVSGRQCVIV
ANDATVKGGTYYPMTVKKHLRAQEVALQNMLPCIYLVDSGGAFLPRQDEVFPDREHFGRIFYNQATMSAKGIPQVAAVLGSCTAGGAYVPAMSDEAVIVR
EQGTIFLGGPPLVKAATGEIVSAEELGGGDLHSRTSGVTDHLADDDEDALRIVRAIADTFGPCEPAQWDVRRSVEPKYPQAELYDVVPPDPRVPYDVHEV
VVRIVDGSEFSEFKAKYGKTLVTAFARVHGHPVGIVANNGVLFSESALKGAHFIELCDKRKIPLLFLQNIAGFMVGRDYEAGGIAKHGAKMVTAVACARV
PKLTVVIGGSYGAGNYSMCGRAYSPRFLWMWPNARISVMGGEQAASVLATVRGEQLSAAGTPWSPDEEEAFKAPIRAQYEDQGNPYYSTARLWDDGIIDP
ADTRTVVGLALSLCAHAPLDQVGYGVFRM

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• data from Culviner et al (2025) (55,259 Mtb clinical isolates)
  • overall pN/pS for Rv2502c: 0.517846277
  • lineage-specific pN/pS in L1: 0.436009025
  • lineage-specific pN/pS in L2: 0.613137692
  • lineage-specific pN/pS in L3: 0.421705562
  • lineage-specific pN/pS in L4: 0.568001832

• Analysis of dN/dS (omega) in a global collection of 10k Mtb clinical isolates using GenomegaMap (Window model)
• clinical isolates collection: global set of 10,626 Mtb genomes
• In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
• A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	global set of 10,626 Mtb clinical isolates
under significant positive selection?	NO
omega peak height (95%CI lower bound)	1.55 (0.6)
codons under selection
omega plots
genetic variants*	link