TB Genome Annotation Portal

Rv0006 (gyrA)

• Current annotations:
  • TBCAP: (community-based annotations - see table at bottom of page)
  • TBDB: DNA gyrase subunit A
  • REFSEQ: DNA gyrase subunit A
  • PATRIC: DNA gyrase subunit A (EC 5.99.1.3)
  • TUBERCULIST: DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
  • NCBI: DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase)
  • updated information (H37Rv4):
    • gene name: gyrA
    • function:
    • reference:
• Type: Not Target
• Start: 7302
• End: 9818
• Operon:


• Trans-membrane region:
  
• Role: II.A.5 - DNA replication, repair, recombination and restriction/modification
• GO terms:
  • GO:0046677 - response to antibiotic (Uniprot)
  • GO:0034335 - DNA supercoiling activity (Uniprot)
  • GO:0016887 - ATPase activity (Uniprot)
  • GO:0016853 - isomerase activity (Uniprot)
  • GO:0006265 - DNA topological change (Uniprot)
  • GO:0006259 - DNA metabolic process (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: 3ilw, 3ifz, 3uc1
• Search for Homologs in PDB
• Top 10 Homologs in PDB (as of Nov 2020):
  

  PDB	aa ident	species	PDB title
  5BTL	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
  5BTD	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  5BS8	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of a topoisomerase II complex
  4G3N	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain at 1.4 A resolution
  3UC1	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis gyrase type IIA topoisomerase C-terminal domain
  3ILW	100%	Mycobacterium tuberculosis	Structure of DNA gyrase subunit A N-terminal domain
  6GAV	99%	Mycobacterium tuberculosis	Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
  6GAU	99%	Mycobacterium tuberculosis	Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert
  3IFZ	99%	Mycobacterium tuberculosis	crystal structure of the first part of the Mycobacterium tuberculosis DNA gyrase reaction core: the breakage and reunion domain at 2.7 A resolution

• Links to additional information on gyrA:
  • TBDB (updated)
  • Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
  • UniProt
  • AlphaFold model
  • Vulnerability = -9.076 (from Jeremy Rock's lab)
  • KEGG - nucleotide and amino acid sequences of gene
  • Mycobrowser
  • PATRIC
  • BioCyc
  • Systems Biology

Amino Acid Sequence

MTDTTLPPDDSLDRIEPVDIEQEMQRSYIDYAMSVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIYDSLVRMA
QPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFIPNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADA
VFWALENHDADEEETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEEDSRGRTSLVITELPYQVNHDNFITSIAEQVRDGKLAGIS
NIEDQSSDRVGLRIVIEIKRDAVAKVVINNLYKHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILRGLVKALDA
LDEVIALIRASETVDIARAGLIELLDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRGIVRDELAEIVDRHGDDRRTRIIA
ADGDVSDEDLIAREDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQGRVYRAKAYDLPEASRTARGQHVANLL
AFQPEERIAQVIQIRGYTDAPYLVLATRNGLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEALRPMGRATSGV
QGMRFNIDDRLLSLNVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKG
VRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQTGN

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?	YES	YES
omega peak height (95%CI lower bound)	6.72 (3.25)	3.06 (1.02)
codons under selection	70, 71, 72, 73, 74, 88, 89, 90, 91, 92, 93, 94, 95	94
omega plots
genetic variants*	link	link
statistics at each codon	link	link