TB Genome Annotation Portal

Rv0005 (gyrB)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: DNA gyrase subunit B
  • REFSEQ: DNA gyrase subunit B
  • PATRIC: DNA gyrase subunit B (EC 5.99.1.3)
  • TUBERCULIST: DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
  • NCBI: DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
  • updated information (H37Rv4):
    • gene name: gyrB
    • function:
    • reference:
• Type: Not Target
• Start: 5240
• End: 7267
• Operon:


• Trans-membrane region:
  
• Role: II.A.5 - DNA replication, repair, recombination and restriction/modification
• GO terms:
  • GO:0046872 - metal ion binding (Uniprot)
  • GO:0046677 - response to antibiotic (Uniprot)
  • GO:0040007 - growth (Uniprot)
  • GO:0034335 - DNA supercoiling activity (Uniprot)
  • GO:0016853 - isomerase activity (Uniprot)
  • GO:0009295 - nucleoid (Uniprot)
  • GO:0007059 - chromosome segregation (Uniprot)
  • GO:0006265 - DNA topological change (Uniprot)
  • GO:0005886 - plasma membrane (Uniprot)
  • GO:0005737 - cytoplasm (Uniprot)
  • GO:0005694 - chromosome (Uniprot)
  • GO:0005618 - cell wall (Uniprot)
  • GO:0005524 - ATP binding (Uniprot)
  • GO:0005515 - protein binding (Uniprot)
  • GO:0003918 - DNA topoisomerase type II (ATP-hydrolyzing) activity (Uniprot)
  • GO:0003916 - DNA topoisomerase activity (Uniprot)
  • GO:0003677 - DNA binding (Uniprot)
  • GO:0000287 - magnesium ion binding (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: 3m4i, 2zjt, 3ig0
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  6GAV	100%	Mycobacterium tuberculosis	Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
  6GAU	100%	Mycobacterium tuberculosis	Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
  5BTN	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTL	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of a topoisomerase II complex
  5BTI	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTG	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTF	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTD	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTC	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BTA	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex

• Links to additional information on gyrB:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -11.389 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • BioCyc
  • Systems Biology
  • Mycobrowser
  • PATRIC

Amino Acid Sequence

VAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVM
TQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFL
NKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSES
VHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANP
TDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNT
EVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKK
INKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV

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)	2.34 (0.84)	2.58 (0.85)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link