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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL2243 [new locus tag: SACOL_RS11800 ]
  • pan locus tag?: SAUPAN005706000
  • symbol: topB
  • pan gene symbol?: topB
  • synonym:
  • product: DNA topoisomerase III

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SACOL2243 [new locus tag: SACOL_RS11800 ]
  • symbol: topB
  • product: DNA topoisomerase III
  • replicon: chromosome
  • strand: -
  • coordinates: 2309871..2312006
  • length: 2136
  • 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
    1981
    2041
    2101
    ATGAAATCTTTAATATTAGCTGAAAAACCATCAGTCGCAAGAGATATTGCTGATGCTTTA
    CAAATAAATCAGAAGCGTAATGGTTACTTTGAAAATAACCAATATATTGTCACGTGGGCG
    TTAGGTCATCTAGTGACAAATGCGACACCTGAACAATACGATAAAAATTTAAAGGAATGG
    CGATTAGAAGACCTTCCAATTATACCTAAATATATGAAAACTGTTGTTATTGGTAAAACA
    AGCAAACAATTTAAAACAGTAAAAGCGTTAATTTTAGATAATAAAGTGAAAGATATTATT
    ATTGCAACAGATGCTGGACGAGAAGGTGAACTAGTTGCAAGATTGATTTTGGATAAAGTT
    GGTAACAAAAAGCCAATCCGTCGATTATGGATTAGCTCAGTTACTAAAAAAGCTATTCAA
    CAAGGTTTTAAAAATTTAAAAGACGGTCGTCAATATAACGATTTGTATTATGCAGCGTTA
    GCGAGAAGTGAGGCAGATTGGATTGTTGGGATTAATGCAACGCGTGCACTAACAACAAAG
    TATGATGCACAGCTATCCCTGGGACGTGTTCAGACACCAACGATTCAATTAGTAAATACA
    CGACAACAAGAGATTAATCAGTTCAAACCACAACAATACTTTACATTATCATTAACGGTA
    AAAGGGTTTGATTTTCAGCTAGAATCAAATCAGCGATATACCAATAAAGAAACTTTAGAA
    CAGATGGTTAATAATTTGAAAAATGTCGATGGTAAGATTAAATCTGTTGCTACTAAACAT
    AAGAAGTCGTATCCGCAATCACTGTACAATTTAACAGATTTACAACAAGATATGTATAGA
    CGTTATAAAATTGGACCTAAAGAAACATTGAATACACTTCAAAGCTTATATGAGAGACAT
    AAAGTCGTAACCTATCCAAGAACAGATTCAAACTATTTAACAACTGATATGGTAGATACT
    ATGAAAGAACGTATTCAGGCGACGATGGCAACAACATATAAAGACCAAGCACGCCCATTA
    ATGTCTAAAACATTTTCATCAAAAATGTCGATATTTAATAATCAAAAAGTATCTGATCAC
    CATGCAATTATTCCTACAGAAGTGAGACCTGTCATGTCAGACTTAAGTAATAGAGAATTA
    AAGTTATACGATATGATTGTCGAGCGTTTTTTAGAAGCTTTAATGCCTCCGCACGAGTAT
    GACGCGATAACTGTAACTTTAGAGGTTGCAGGGCACACATTTGTTTTGAAAGAGAATGTA
    ACAACTGTTTTAGGTTTTAAATCTATTAGACAAGGTGAATCTATTACAGAGATGCAACAG
    CCTTTTTCAGAAGGCGATGAAGTGAAGATTTCAAAAACAAATATTAGAGAACATGAAACA
    ACACCTCCAGAATATTTTAATGAAGGTTCGTTATTAAAAGCGATGGAGAACCCTCAGAAC
    TTTATTCAATTGAAGGATAAAAAATATGCGCAAACTTTAAAACAAACAGGTGGTATCGGC
    ACAGTTGCAACAAGGGCCGACATTATCGATAAATTATTTAATATGAATGCCATTGAATCA
    AGAGACGGTAAAATTAAAGTAACGTCAAAAGGTAAACAAATATTAGAATTAGCACCAGAA
    GAATTAACGTCGCCACTTTTAACTGCACAATGGGAAGAAAAATTACTTTTAATTGAACGT
    GGTAAATATCAGGCGAAAACATTTATTAATGAAATGAAAGATTTTACGAAAGATGTTGTA
    AATGGGATTAAAAATAGTGATCGTAAATATAAACACGATAATTTAACAACCACAGAATGC
    CCAACGTGTGGTAAATTCATGATTAAAGTTAAAACTAAAAATGGTCAGATGCTTGTGTGC
    CAAGATCCATCTTGTAAGACGAAAAAGAATGTACAGCGCAAAACAAATGCAAGATGTCCA
    AACTGTAAAAAGAAATTAACGTTGTTTGGTAAAGGGAAAGAAGCGGTATATCGTTGTGTT
    TGTGGACATTCTGAAACGCAAGCACATATGGATCAGCGTATGAAGTCTAAATCCTCTGGT
    AAAGTATCTCGTAAAGAAATGAAAAAGTATATGAATAAAAATGAAGGTTTAGACAATAAT
    CCGTTTAAAGATGCATTAAAGAACTTGAATTTATAG
    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
    1980
    2040
    2100
    2136

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SACOL2243 [new locus tag: SACOL_RS11800 ]
  • symbol: TopB
  • description: DNA topoisomerase III
  • length: 711
  • theoretical pI: 10.0831
  • theoretical MW: 81523.4
  • GRAVY: -0.657806

Function[edit source | edit]

  • reaction:
    EC 5.99.1.2?  ExPASy
    DNA topoisomeraseATP-independent breakage of single-stranded DNA, followed by passage and rejoining
  • TIGRFAM:
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase III (TIGR01056; EC 5.99.1.2; HMM-score: 674.4)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase I (TIGR01057; EC 5.99.1.2; HMM-score: 262.4)
    Genetic information processingDNA metabolismDNA replication, recombination, and repairDNA topoisomerase I (TIGR01051; EC 5.99.1.2; HMM-score: 206.7)
    conserved hypothetical protein (TIGR02443; HMM-score: 14.8)
    Genetic information processingProtein fateProtein modification and repairhydrogenase nickel insertion protein HypA (TIGR00100; HMM-score: 7.2)
  • TheSEED:  
    DNA MetabolismDNA uptake, competenceDNA processing cluster DNA topoisomerase III (EC 5.99.1.2) 
  • PFAM:
    no clan definedTopoisom_bac; DNA topoisomerase (PF01131; HMM-score: 371.4)
    Toprim-like (CL0413) Toprim; Toprim domain (PF01751; HMM-score: 57.3)
    Zn_Beta_Ribbon (CL0167) zf-C4_Topoisom; Topoisomerase DNA binding C4 zinc finger (PF01396; HMM-score: 18.2)
    DUF2387; Probable metal-binding protein (DUF2387) (PF09526; HMM-score: 14.2)
    zf-ribbon_3; zinc-ribbon domain (PF13248; HMM-score: 14)
    Toprim-like (CL0413) Toprim_4; Toprim domain (PF13662; HMM-score: 13)
    no clan definedPXA; PXA domain (PF02194; HMM-score: 12.7)
    DUF5416; Family of unknown function (DUF5416) (PF17437; HMM-score: 12.2)
    4H_Cytokine (CL0053) Leptin; Leptin (PF02024; HMM-score: 11.1)
    no clan definedDNA_ligase_ZBD; NAD-dependent DNA ligase C4 zinc finger domain (PF03119; HMM-score: 10.1)
    HypA; Hydrogenase/urease nickel incorporation, metallochaperone, hypA (PF01155; HMM-score: 9.8)
    Zn_Beta_Ribbon (CL0167) zinc-ribbons_6; zinc-ribbons (PF07191; HMM-score: 9.5)
    zf-TFIIB; Transcription factor zinc-finger (PF13453; HMM-score: 7.1)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors: Mg2+
  • effectors:
  • protein partners:
    SACOL1513(hup)DNA-binding protein HU  [1] (data from MRSA252)
    SACOL1727(infC)translation initiation factor IF-3  [1] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [1] (data from MRSA252)
    SACOL0584(rplA)50S ribosomal protein L1  [1] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SACOL2239(rplC)50S ribosomal protein L3  [1] (data from MRSA252)
    SACOL2238(rplD)50S ribosomal protein L4  [1] (data from MRSA252)
    SACOL2227(rplE)50S ribosomal protein L5  [1] (data from MRSA252)
    SACOL2224(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SACOL2220(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    SACOL2232(rplP)50S ribosomal protein L16  [1] (data from MRSA252)
    SACOL1257(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    SACOL1725(rplT)50S ribosomal protein L20  [1] (data from MRSA252)
    SACOL1702(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SACOL2234(rplV)50S ribosomal protein L22  [1] (data from MRSA252)
    SACOL2237(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [1] (data from MRSA252)
    SACOL1769(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    SACOL2222(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SACOL0437(rpsF)30S ribosomal protein S6  [1] (data from MRSA252)
    SACOL0592(rpsG)30S ribosomal protein S7  [1] (data from MRSA252)
    SACOL2206(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    SACOL2214(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    SACOL2230(rpsQ)30S ribosomal protein S17  [1] (data from MRSA252)
    SACOL2235(rpsS)30S ribosomal protein S19  [1] (data from MRSA252)
    SACOL1448(sucB)dihydrolipoamide succinyltransferase  [1] (data from MRSA252)
    SACOL03035'-nucleotidase  [1] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [1] (data from MRSA252)
    SACOL1753universal stress protein  [1] (data from MRSA252)
    SACOL2072DEAD/DEAH box helicase  [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: 0.143
    • Ymax_pos: 20
    • Cmax: 0.155
    • Cmax_pos: 54
    • Smax: 0.213
    • Smax_pos: 17
    • Smean: 0.166
    • D: 0.152
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MKSLILAEKPSVARDIADALQINQKRNGYFENNQYIVTWALGHLVTNATPEQYDKNLKEWRLEDLPIIPKYMKTVVIGKTSKQFKTVKALILDNKVKDIIIATDAGREGELVARLILDKVGNKKPIRRLWISSVTKKAIQQGFKNLKDGRQYNDLYYAALARSEADWIVGINATRALTTKYDAQLSLGRVQTPTIQLVNTRQQEINQFKPQQYFTLSLTVKGFDFQLESNQRYTNKETLEQMVNNLKNVDGKIKSVATKHKKSYPQSLYNLTDLQQDMYRRYKIGPKETLNTLQSLYERHKVVTYPRTDSNYLTTDMVDTMKERIQATMATTYKDQARPLMSKTFSSKMSIFNNQKVSDHHAIIPTEVRPVMSDLSNRELKLYDMIVERFLEALMPPHEYDAITVTLEVAGHTFVLKENVTTVLGFKSIRQGESITEMQQPFSEGDEVKISKTNIREHETTPPEYFNEGSLLKAMENPQNFIQLKDKKYAQTLKQTGGIGTVATRADIIDKLFNMNAIESRDGKIKVTSKGKQILELAPEELTSPLLTAQWEEKLLLIERGKYQAKTFINEMKDFTKDVVNGIKNSDRKYKHDNLTTTECPTCGKFMIKVKTKNGQMLVCQDPSCKTKKNVQRKTNARCPNCKKKLTLFGKGKEAVYRCVCGHSETQAHMDQRMKSKSSGKVSRKEMKKYMNKNEGLDNNPFKDALKNLNL

Experimental data[edit source | edit]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [2] [3]
    quantitative data / protein copy number per cell: 90 [4]

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: no data available

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. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 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. 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)
  4. 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)

Relevant publications[edit source | edit]