TB Genome Annotation Portal

Rv3080c (pknK)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: serine/threonine-protein kinase pknK
  • REFSEQ: serine/threonine-protein kinase transcriptional regulatory protein
  • PATRIC: Transcriptional activator of maltose regulon MalT
  • TUBERCULIST: Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)
  • NCBI: Serine/threonine-protein kinase transcriptional regulatory protein PknK (protein kinase K) (STPK K)
  • updated information (H37Rv4):
    • gene name: pknK
    • function:
    • reference:
• Type: Not Target
• Start: 3442656
• End: 3445988
• Operon:


• Trans-membrane region:
  
• Role: I.J.3 - Serine-Threonine protein kinases and phosphoprotein phosphatases
• GO terms:
  • GO:0051090 - regulation of DNA binding transcription factor activity (Uniprot)
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0046777 - protein autophosphorylation (Uniprot)
  • GO:0042802 - identical protein binding (Uniprot)
  • GO:0016740 - transferase activity (Uniprot)
  • GO:0016310 - phosphorylation (Uniprot)
  • GO:0016301 - kinase activity (Uniprot)
  • GO:0016020 - membrane (Uniprot)
  • GO:0009405 - pathogenesis (Uniprot)
  • GO:0006468 - protein phosphorylation (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005829 - cytosol (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005576 - extracellular region (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0004674 - protein serine/threonine kinase activity (Uniprot)
  • GO:0004672 - protein kinase 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
  6B2P	36%	Mycobacterium tuberculosis	Dual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis
  5U94	36%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of the Mycobacterium tuberculosis PASTA kinase PknB in complex with the potential theraputic kinase inhibitor GSK690693.
  3ORM	36%	Mycobacterium tuberculosis	Mycobacterium tuberculosis PknB kinase domain D76A mutant
  3F69	36%	Mycobacterium tuberculosis	Crystal structure of the Mycobacterium tuberculosis PknB mutant kinase domain in complex with KT5720
  2FUM	36%	Mycobacterium tuberculosis H37Rv	Catalytic domain of protein kinase PknB from Mycobacterium tuberculosis in complex with mitoxantrone
  1O6Y	36%	MYCOBACTERIUM TUBERCULOSIS	Catalytic domain of PknB kinase from Mycobacterium tuberculosis
  1MRU	36%	Mycobacterium tuberculosis	Intracellular Ser/Thr protein kinase domain of Mycobacterium tuberculosis PknB.
  6I2P	36%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of the Mycobacterium tuberculosis PknB kinase domain (L33E mutant) in complex with its substrate GarA
  3ORT	36%	Mycobacterium tuberculosis	Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 6)
  3ORP	36%	Mycobacterium tuberculosis	Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 5)

• Links to additional information on pknK:
  • 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 = 1.053 (from Jeremy Rock's lab)

Amino Acid Sequence

MTDVDPHATRRDLVPNIPAELLEAGFDNVEEIGRGGFGVVYRCVQPSLDRAVAVKVLSTDLDRDNLERFLREQRAMGRLSGHPHIVTVLQVGVLAGGRPF
IVMPYHAKNSLETLIRRHGPLDWRETLSIGVKLAGALEAAHRVGTLHRDVKPGNILLTDYGEPQLTDFGIARIAGGFETATGVIAGSPAFTAPEVLEGAS
PTPASDVYSLGATLFCALTGHAAYERRSGERVIAQFLRITSQPIPDLRKQGLPADVAAAIERAMARHPADRPATAADVGEELRDVQRRNGVSVDEMPLPV
ELGVERRRSPEAHAAHRHTGGGTPTVPTPPTPATKYRPSVPTGSLVTRSRLTDILRAGGRRRLILIHAPSGFGKSTLAAQWREELSRDGAAVAWLTIDND
DNNEVWFLSHLLESIRRVRPTLAESLGHVLEEHGDDAGRYVLTSLIDEIHENDDRIAVVIDDWHRVSDSRTQAALGFLLDNGCHHLQLIVTSWSRAGLPV
GRLRIGDELAEIDSAALRFDTDEAAALLNDAGGLRLPRADVQALTTSTDGWAAALRLAALSLRGGGDATQLLRGLSGASDVIHEFLSENVLDTLEPELRE
FLLVASVTERTCGGLASALAGITNGRAMLEEAEHRGLFLQRTEDDPNWFRFHQMFADFLHRRLERGGSHRVAELHRRASAWFAENGYLHEAVDHALAAGD
PARAVDLVEQDETNLPEQSKMTTLLAIVQKLPTSMVVSRARLQLAIAWANILLQRPAPATGALNRFETALGRAELPEATQADLRAEADVLRAVAEVFADR
VERVDDLLAEAMSRPDTLPPRVPGTAGNTAALAAICRFEFAEVYPLLDWAAPYQEMMGPFGTVYAQCLRGMAARNRLDIVAALQNFRTAFEVGTAVGAHS
HAARLAGSLLAELLYETGDLAGAGRLMDESYLLGSEGGAVDYLAARYVIGARVKAAQGDHEGAADRLSTGGDTAVQLGLPRLAARINNERIRLGIALPAA
VAADLLAPRTIPRDNGIATMTAELDEDSAVRLLSAGDSADRDQACQRAGALAAAIDGTRRPLAALQAQILHIETLAATGRESDARNELAPVATKCAELGL
SRLLVDAGLA

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)	1.85 (0.56)	1.34 (0.62)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link