TB Genome Annotation Portal

Rv2457c (clpX)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: ATP-dependent Clp protease ATP-binding subunit ClpX
  • REFSEQ: ATP-dependent protease ATP-binding subunit ClpX
  • PATRIC: ATP-dependent Clp protease ATP-binding subunit ClpX
  • TUBERCULIST: Probable ATP-dependent CLP protease ATP-binding subunit ClpX
  • NCBI: Probable ATP-dependent CLP protease ATP-binding subunit ClpX
  • updated information (H37Rv4):
    • gene name: clpX
    • function:
    • reference:
• Type: Not Target
• Start: 2758208
• End: 2759488
• Operon:


• Trans-membrane region:
  
• Role: II.B.3 - Proteins, peptides and glycopeptides
• GO terms:
  • GO:0051301 - cell division (Uniprot)
  • GO:0051082 - unfolded protein binding (Uniprot)
  • GO:0046983 - protein dimerization activity (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0032272 - negative regulation of protein polymerization (Uniprot)
  • GO:0030163 - protein catabolic process (Uniprot)
  • GO:0008270 - zinc ion binding (Uniprot)
  • GO:0006508 - proteolysis (Uniprot)
  • GO:0006457 - protein folding (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0004176 - ATP-dependent peptidase activity (Uniprot)
  • GO:0000166 - nucleotide binding (Uniprot)
• Reaction(s) (based on iSM810 metabolic model):
• 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
  2DS8	76%	Escherichia coli	Structure of the ZBD-XB complex
  2DS6	76%	Escherichia coli	Structure of the ZBD in the tetragonal crystal form
  2DS5	76%	Escherichia coli	Structure of the ZBD in the orthorhomibic crystal from
  1OVX	76%	Escherichia coli	NMR structure of the E. coli ClpX chaperone zinc binding domain dimer
  2DS7	73%	Escherichia coli	Structure of the ZBD in the hexagonal crystal form
  6SFW	66%	Listeria monocytogenes	Cryo-EM Structure of the ClpX component of the ClpXP1/2 degradation machinery.
  6WSG	62%	Escherichia coli	ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex
  6WRF	62%	Escherichia coli (strain K12)	ClpX-ClpP complex bound to GFP-ssrA, recognition complex
  6WR2	62%	Escherichia coli (strain K12)	ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP
  4I9K	62%	Escherichia coli	Crystal structure of symmetric W-W-W ClpX Hexamer

• Links to additional information on clpX:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -6.615 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MARIGDGGDLLKCSFCGKSQKQVKKLIAGPGVYICDECIDLCNEIIEEELADADDVKLDELPKPAEIREFLEGYVIGQDTAKRTLAVAVYNHYKRIQAGE
KGRDSRCEPVELTKSNILMLGPTGCGKTYLAQTLAKMLNVPFAIADATALTEAGYVGEDVENILLKLIQAADYDVKRAETGIIYIDEVDKIARKSENPSI
TRDVSGEGVQQALLKILEGTQASVPPQGGRKHPHQEFIQIDTTNVLFIVAGAFAGLEKIIYERVGKRGLGFGAEVRSKAEIDTTDHFADVMPEDLIKFGL
IPEFIGRLPVVASVTNLDKESLVKILSEPKNALVKQYIRLFEMDGVELEFTDDALEAIADQAIHRGTGARGLRAIMEEVLLPVMYDIPSRDDVAKVVVTK
ETVQDNVLPTIVPRKPSRSERRDKSA

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)	1.16 (0.12)	1.44 (0.45)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link