TB Genome Annotation Portal

Rv0016c (pbpA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: penicillin-binding protein A
  • REFSEQ: penicillin-binding protein PbpA
  • PATRIC: Cell division protein FtsI [Peptidoglycan synthetase] (EC 2.4.1.129)
  • TUBERCULIST: Probable penicillin-binding protein PbpA
  • NCBI: Probable penicillin-binding protein PbpA
  • updated information (H37Rv4):
    • gene name: pbpA
    • function:
    • reference:
• Type: Not Target
• Start: 18759
• End: 20234
• Operon:


• Trans-membrane region:
  
• Role: II.C.3 - Murein sacculus and peptidoglycan
• GO terms:
  • GO:0071555 - cell wall organization (Uniprot)
  • GO:0016021 - integral component of membrane (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0009252 - peptidoglycan biosynthetic process (Uniprot)
  • GO:0008658 - penicillin binding (Uniprot)
  • GO:0008360 - regulation of cell shape (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (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: 3upo, 3upn, 3un7, 3lo7, 3upp
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  3LO7	100%	Mycobacterium tuberculosis	Crystal structure of PBPA from Mycobacterium tuberculosis
  3UPP	99%	Mycobacterium tuberculosis	Structure of penicillin-binding protein A from M. tuberculosis: ceftrixaone acyl-enzyme complex
  3UPO	99%	Mycobacterium tuberculosis	Structure of penicillin-binding protein A from M. tuberculosis: penicillin G acyl-enzyme complex
  3UPN	99%	Mycobacterium tuberculosis	Structure of penicillin-binding protein A from M. tuberculosis: imipenem acyl-enzyme complex
  3UN7	99%	Mycobacterium tuberculosis	Crystal structure of PBPA from MYCOBACTERIUM TUBERCULOSIS

• Links to additional information on pbpA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -0.256 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MNASLRRISVTVMALIVLLLLNATMTQVFTADGLRADPRNQRVLLDEYSRQRGQITAGGQLLAYSVATDGRFRFLRVYPNPEVYAPVTGFYSLRYSSTAL
ERAEDPILNGSDRRLFGRRLADFFTGRDPRGGNVDTTINPRIQQAGWDAMQQGCYGPCKGAVVALEPSTGKILALVSSPSYDPNLLASHNPEVQAQAWQR
LGDNPASPLTNRAISETYPPGSTFKVITTAAALAAGATETEQLTAAPTIPLPGSTAQLENYGGAPCGDEPTVSLREAFVKSCNTAFVQLGIRTGADALRS
MARAFGLDSPPRPTPLQVAESTVGPIPDSAALGMTSIGQKDVALTPLANAEIAATIANGGITMRPYLVGSLKGPDLANISTTVGYQQRRAVSPQVAAKLT
ELMVGAEKVAQQKGAIPGVQIASKTGTAEHGTDPRHTPPHAWYIAFAPAQAPKVAVAVLVENGADRLSATGGALAAPIGRAVIEAALQGEP

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)	2.3 (0.6)	2.13 (0.87)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link