TB Genome Annotation Portal

Rv2496c (bkdB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: pyruvate dehydrogenase E1 component subunit beta
  • REFSEQ: pyruvate dehydrogenase E1 component beta subunit PdhB
  • PATRIC: Branched-chain alpha-keto acid dehydrogenase E1 component beta subunit (EC 1.2.4.4)
  • TUBERCULIST: Probable branched-chain keto acid dehydrogenase E1 component beta subunit BkdB
  • NCBI: Probable branched-chain keto acid dehydrogenase E1 component, beta subunit BkdB
  • updated information (H37Rv4):
    • gene name: bkdB
    • function:
    • reference:
• Type: Not Target
• Start: 2809936
• End: 2810982
• Operon:


• Trans-membrane region:
  
• Role: I.B.2 - Pyruvate dehydrogenase
• GO terms:
  • GO:0055114 - oxidation-reduction process (Uniprot)
  • GO:0016491 - oxidoreductase activity (Uniprot)
  • GO:0008152 - metabolic process (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003863 - 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (Uniprot)
  • GO:0003824 - catalytic activity (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
  • LIPO[c] + OXOMETHYLPENTANOATE[c] -> CO2[c] + 2MBUTLIPO[c]
  • LIPO[c] + MOP[c] -> CO2[c] + 3MBUTLIPO[c]
  • LIPO[c] + OMVAL[c] -> CO2[c] + IBUTLIPO[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
  1UMD	48%	Thermus thermophilus	branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as an intermediate
  1UMC	48%	Thermus thermophilus	branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methylpentanoate
  1UMB	48%	Thermus thermophilus	branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 in holo-form
  1UM9	48%	Thermus thermophilus	branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 in apo-form
  3DVA	47%	Bacillus stearothermophilus	Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
  3DV0	47%	Bacillus stearothermophilus	Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
  3DUF	47%	Bacillus stearothermophilus	Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex
  1W88	47%	GEOBACILLUS STEAROTHERMOPHILUS	The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2
  1W85	47%	GEOBACILLUS STEAROTHERMOPHILUS	The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
  2BP7	43%	PSEUDOMONAS PUTIDA	New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)

• Links to additional information on bkdB:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = 0.025 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTQIADRPARPDETLAVAVSDITQSLTMVQAINRALYDAMAADERVLVFGEDVAVEGGVFRVTEGLADTFGADRCFDTPLAESAIIGIAVGLALRGFVPV
PEIQFDGFSYPAFDQVVSHLAKYRTRTRGEVDMPVTVRIPSFGGIGAAEHHSDSTESYWVHTAGLKVVVPSTPGDAYWLLRHAIACPDPVMYLEPKRRYH
GRGMVDTSRPEPPIGHAMVRRSGTDVTVVTYGNLVSTALSSADTAEQQHDWSLEVIDLRSLAPLDFDTIAASIQRTGRCVVMHEGPRSLGYGAGLAARIQ
EEMFYQLEAPVLRACGFDTPYPPARLEKLWLPGPDRLLDCVERVLRQP

Additional Information

Analysis of Positive Selection in Clinical Isolates *new*

• Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
  • Moldova: 2,057 clinical isolates
  • global set: 5,195 clinical isolates from 15 other countries
• 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.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.57 (0.31)	1.14 (0.5)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link