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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0005 [new locus tag: SACOL_RS00045 ]
  • pan locus tag?: SAUPAN000011000
  • symbol: gyrB
  • pan gene symbol?: gyrB
  • synonym:
  • product: DNA gyrase, B subunit

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL0005 [new locus tag: SACOL_RS00045 ]
  • symbol: gyrB
  • product: DNA gyrase, B subunit
  • replicon: chromosome
  • strand: +
  • coordinates: 5061..6995
  • length: 1935
  • essential: unknown other strains

Accession numbers[edit source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    961
    1021
    1081
    1141
    1201
    1261
    1321
    1381
    1441
    1501
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    ATGGTGACTGCATTGTCAGATGTAAACAACACGGATAATTATGGTGCTGGGCAAATACAA
    GTATTAGAAGGTTTAGAAGCAGCACGTAAAAGACCAGGTATGTATATAGGATCGACTTCA
    GAGAGAGGTTTGCACCATTTAGTGTGGGAAATTGTCGATAATAGTATCGATGAAGCATTA
    GCTGGTTATGCAAATCAAATTGAAGTTGTTATTGAAAAAGATAACTGGATTAAAGTAACG
    GATAACGGACGTGGTATCCCAGTTGATATTCAAGAAAAAATGGGACGTCCAGCTGTCGAA
    GTTATTTTAACTGTTTTACATGCTGGTGGTAAATTTGGCGGTGGCGGATACAAAGTATCT
    GGTGGTTTACATGGTGTTGGTTCATCAGTTGTAAACGCATTGTCACAAGACTTAGAAGTA
    TATGTACACAGAAATGAGACTATATATCATCAAGCATATAAAAAAGGTGTACCTCAATTT
    GACTTAAAAGAAGTTGGCACAACTGATAAGACAGGTACTGTCATTCGTTTTAAAGCAGAT
    GGAGAAATCTTCACAGAGACAACTGTATACAACTATGAAACATTACAGCAGCGTATTAGA
    GAGCTTGCTTTCTTAAACAAAGGAATTCAAATCACATTAAGAGATGAACGTGATGAAGAA
    AACGTTAGAGAAGACTCCTATCACTATGAGGGCGGTATTAAATCGTACGTTGAGTTATTG
    AACGAAAATAAAGAACCTATTCATGATGAGCCAATTTATATTCATCAATCTAAAGATGAT
    ATTGAAGTAGAAATTGCGATTCAATATAACTCAGGATATGCCACAAATCTTTTAACTTAC
    GCAAATAACATTCATACGTATGAAGGTGGTACGCATGAAGACGGATTCAAACGTGCATTA
    ACGCGTGTCTTAAATAGTTATGGTTTAAGTAGCAAGATTATGAAAGAAGAAAAAGATAGA
    CTTTCTGGTGAAGATACACGTGAAGGTATGACAGCAATTATATCTATCAAACATGGTGAT
    CCTCAATTCGAAGGTCAAACGAAGACAAAATTAGGTAATTCTGAAGTGCGTCAAGTTGTA
    GATAAATTATTCTCAGAGCACTTTGAACGATTTTTATATGAAAATCCACAAGTCGCACGT
    ACAGTGGTTGAAAAAGGTATTATGGCGGCACGTGCACGTGTTGCTGCGAAAAAAGCGCGT
    GAAGTAACACGTCGTAAATCAGCGTTAGATGTAGCAAGCCTTCCAGGTAAATTAGCCGAT
    TGCTCTAGTAAAAGTCCTGAAGAATGTGAGATTTTCTTAGTCGAAGGGGACTCTGCCGGG
    GGGTCTACAAAATCTGGTCGTGACTCTAGAACGCAGGCGATTTTACCATTACGAGGTAAG
    ATATTAAATGTTGAAAAAGCACGATTAGATAGAATTTTGAATAACAATGAAATTCGTCAA
    ATGATCACAGCATTTGGTACAGGAATCGGTGGCGACTTTGATCTAGCGAAAGCAAGATAT
    CACAAAATCGTCATTATGACTGATGCCGATGTGGATGGAGCGCATATTAGAACATTGTTA
    TTAACATTCTTCTATCGATTTATGAGACCGTTAATTGAAGCAGGCTATGTGTATATTGCA
    CAGCCACCGTTGTATAAACTGACACAAGGTAAACAAAAGTATTATGTATACAATGATAGG
    GAACTTGATAAACTTAAATCTGAATTGAATCCAACACCAAAATGGTCTATTGCACGATAC
    AAAGGTCTTGGAGAAATGAATGCAGATCAATTATGGGAAACAACAATGAACCCTGAGCAC
    CGCGCTCTTTTACAAGTAAAACTTGAAGATGCGATTGAAGCGGACCAAACATTTGAAATG
    TTAATGGGTGACGTTGTAGAAAACCGTAGACAATTTATAGAAGATAATGCAGTTTATGCA
    AACTTAGACTTCTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1560
    1620
    1680
    1740
    1800
    1860
    1920
    1935

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SACOL0005 [new locus tag: SACOL_RS00045 ]
  • symbol: GyrB
  • description: DNA gyrase, B subunit
  • length: 644
  • theoretical pI: 5.68145
  • theoretical MW: 72511.3
  • GRAVY: -0.493634

Function[edit source | edit]

  • reaction:
    EC 5.99.1.3?  ExPASy
    DNA topoisomerase (ATP-hydrolyzing)ATP-dependent breakage, passage and rejoining of double-stranded DNA
  • TIGRFAM:
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA gyrase, B subunit (TIGR01059; EC 5.99.1.3; HMM-score: 991.1)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase IV, B subunit (TIGR01058; EC 5.99.1.-; HMM-score: 825.2)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase IV, B subunit (TIGR01055; EC 5.99.1.-; HMM-score: 602.9)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA mismatch repair protein MutL (TIGR00585; HMM-score: 20.1)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase VI, B subunit (TIGR01052; EC 5.99.1.3; HMM-score: 15.9)
  • TheSEED:  
    DNA MetabolismDNA replicationDNA topoisomerases, Type II, ATP-dependent DNA gyrase subunit B (EC 5.99.1.3) 
    Virulence, Disease and DefenseResistance to antibiotics and toxic compoundsResistance to fluoroquinolones DNA gyrase subunit B (EC 5.99.1.3) 
    Cell Division Subsystem including YidCD DNA gyrase subunit B (EC 5.99.1.3) 
  • PFAM:
    S5 (CL0329) DNA_gyraseB; DNA gyrase B (PF00204; HMM-score: 211.1)
    no clan definedDNA_gyraseB_C; DNA gyrase B subunit, carboxyl terminus (PF00986; HMM-score: 103.5)
    His_Kinase_A (CL0025) HATPase_c; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (PF02518; HMM-score: 77.7)
    Toprim-like (CL0413) Toprim; Toprim domain (PF01751; HMM-score: 63)
    His_Kinase_A (CL0025) HATPase_c_3; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (PF13589; HMM-score: 20.6)
    no clan definedTOPRIM_C; C-terminal associated domain of TOPRIM (PF16898; HMM-score: 16.1)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors: Ca2+, Mg2+, Mn2+
  • effectors:
  • protein partners:
    SACOL0593(fusA)elongation factor G  [1] (data from MRSA252)
    SACOL0006(gyrA)DNA gyrase, A subunit  [1] (data from MRSA252)
    SACOL1288(infB)translation initiation factor IF-2  [1] (data from MRSA252)
    SACOL1745(pyk)pyruvate kinase  [1] (data from MRSA252)

Localization[edit source | edit]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • Internal Helices: 0
  • LocateP: Intracellular
    • Prediction by SwissProt Classification: Cytoplasmic
    • Pathway Prediction: No pathway
    • Intracellular Possibility: 1
    • Signal Peptide Possibility: -1
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: No CleavageSite
  • SignalP: no predicted signal peptide
    • Ymax: 0.104
    • Ymax_pos: 28
    • Cmax: 0.124
    • Cmax_pos: 16
    • Smax: 0.129
    • Smax_pos: 27
    • Smean: 0.081
    • D: 0.095
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MVTALSDVNNTDNYGAGQIQVLEGLEAARKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTVLHAGGKFGGGGYKVSGGLHGVGSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYEGGIKSYVELLNENKEPIHDEPIYIHQSKDDIEVEIAIQYNSGYATNLLTYANNIHTYEGGTHEDGFKRALTRVLNSYGLSSKIMKEEKDRLSGEDTREGMTAIISIKHGDPQFEGQTKTKLGNSEVRQVVDKLFSEHFERFLYENPQVARTVVEKGIMAARARVAAKKAREVTRRKSALDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKLKSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNAVYANLDF

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3] [4]
    quantitative data / protein copy number per cell: 215 [5]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

Protein synthesis (provided by Aureolib)[edit source | edit]

Protein stability[edit source | edit]

  • half-life: 61.35 h [6]

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  1. 1.0 1.1 1.2 1.3 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
    Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
    J. Proteome Res.: 2011, 10(3);1139-50
    [PubMed:21166474] [WorldCat.org] [DOI] (I p)
  2. Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS ONE: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  3. Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J. Proteome Res.: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  4. Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int. J. Med. Microbiol.: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)
  5. Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)
  6. Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol. Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

Relevant publications[edit source | edit]