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NCBI: 03-AUG-2016

Summary[edit source | edit]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_01263
  • pan locus tag?: SAUPAN003588000
  • symbol: SAOUHSC_01263
  • pan gene symbol?: rny/cvfA
  • synonym:
  • product: phosphodiesterase

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SAOUHSC_01263
  • symbol: SAOUHSC_01263
  • product: phosphodiesterase
  • replicon: chromosome
  • strand: +
  • coordinates: 1217620..1219179
  • length: 1560
  • essential: no [1] DEG 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
    GTGAATTTATTAAGCCTCCTACTCATTTTGCTGGGGATCATTCTAGGAGTTGTTGGAGGG
    TATGTTGTTGCCCGAAATTTGTTGCTTCAAAAGCAATCACAAGCTAGACAAACTGCCGAA
    GATATTGTAAATCAAGCACATAAAGAAGCTGACAATATCAAAAAAGAGAAATTACTTGAG
    GCAAAAGAAGAAAACCAAATCCTAAGAGAACAAACTGAAGCAGAACTACGAGAAAGACGT
    AGCGAACTTCAAAGACAAGAAACCCGACTTCTTCAAAAAGAAGAAAACTTAGAGCGCAAA
    TCTGATCTATTAGATAAAAAAGATGAGATTTTAGAGCAAAAAGAATCAAAAATTGAAGAA
    AAACAACAACAAGTAGATGCAAAAGAGAGTAGTGTTCAAACGTTAATAATGAAGCATGAA
    CAAGAATTAGAACGCATCTCCGGTCTCACTCAAGAAGAAGCTATTAATGAGCAACTTCAA
    AGAGTAGAGGAAGAACTGTCACAAGATATTGCAGTACTTGTTAAAGAAAAAGAAAAAGAA
    GCTAAAGAAAAAGTTGATAAAACAGCAAAAGAATTATTAGCTACAGCAGTACAAAGATTA
    GCAGCAGATCACACAAGTGAATCAACGGTATCAGTAGTTAACTTACCTAATGATGAGATG
    AAAGGTCGAATCATTGGACGAGAAGGACGAAACATCCGCACACTTGAAACTTTAACTGGC
    ATTGATTTAATTATTGATGACACACCAGAAGCGGTTATATTATCTGGTTTTGATCCAATA
    AGAAGAGAAATTGCTAGAACAGCACTTGTTAACTTAGTATCTGATGGACGTATTCATCCA
    GGTAGAATTGAAGATATGGTCGAAAAAGCTAGAAAAGAAGTAGACGATATTATTAGAGAA
    GCAGGTGAACAAGCTACATTTGAAGTGAACGCACATAATATGCATCCTGACTTAGTAAAA
    ATTGTAGGGCGTTTAAACTATCGTACGAGTTACGGTCAAAATGTACTTAAACATTCAATT
    GAAGTTGCGCATCTTGCTAGTATGTTAGCTGCTGAGCTAGGCGAAGATGAGACATTAGCG
    AAACGAGCTGGACTTTTACATGATGTTGGTAAAGCAATTGATCATGAAGTAGAAGGTAGT
    CATGTTGAAATCGGTGTAGAATTAGCGAAAAAATATGGTGAAAATGAAACAGTTATTAAT
    GCAATCCATTCTCATCATGGTGATGTTGAACCTACATCTATTATATCTATCCTTGTTGCT
    GCTGCAGATGCATTGTCTGCGGCTCGTCCAGGTGCAAGAAAAGAAACATTAGAGAATTAT
    ATTCGTCGATTAGAACGTTTAGAAACGTTATCAGAAAGTTATGATGGTGTAGAAAAAGCA
    TTTGCGATTCAGGCAGGTAGAGAAATCCGAGTGATTGTATCTCCTGAAGAAATTGATGAT
    TTAAAATCTTATCGATTGGCTAGAGATATTAAAAATCAGATTGAAGATGAATTACAATAT
    CCTGGTCATATCAAGGTGACAGTTGTTCGAGAGACTAGAGCAGTAGAATATGCGAAATAA
    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

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SAOUHSC_01263
  • symbol: SAOUHSC_01263
  • description: phosphodiesterase
  • length: 519
  • theoretical pI: 4.9413
  • theoretical MW: 58511.8
  • GRAVY: -0.519268

Function[edit source | edit]

  • reaction:
    EC 3.1.-.-?  ExPASy
  • TIGRFAM:
    Genetic information processingTranscriptionDegradation of RNAribonuclease Y (TIGR03319; EC 3.1.-.-; HMM-score: 795.6)
    HDIG domain (TIGR00277; HMM-score: 86.3)
    arCOG04150 universal archaeal KH domain protein (TIGR03665; HMM-score: 27.1)
    Unknown functionEnzymes of unknown specificityputative HD superfamily hydrolase (TIGR00488; HMM-score: 26.4)
    NusA family KH domain protein, archaeal (TIGR01952; HMM-score: 18.2)
    CRISPR-associated endonuclease Cas3-HD (TIGR01596; EC 3.1.-.-; HMM-score: 17.9)
    MetabolismTransport and binding proteinsCations and iron carrying compoundspotassium uptake protein, Trk family (TIGR00934; HMM-score: 3.3)
  • TheSEED:  
    CBSS-257314.1.peg.676 Ribonuclease Y 
  • PFAM:
    no clan definedDUF3552; Domain of unknown function (DUF3552) (PF12072; HMM-score: 212.2)
    HD_PDEase (CL0237) HD; HD domain (PF01966; HMM-score: 69.3)
    HDOD; HDOD domain (PF08668; HMM-score: 29.9)
    KH (CL0007) KH_1; KH domain (PF00013; HMM-score: 29.3)
    KH_4; KH domain (PF13083; HMM-score: 21.8)
    KH_2; KH domain (PF07650; HMM-score: 14.4)
    no clan definedUPF0242; Uncharacterised protein family (UPF0242) (PF06785; HMM-score: 8.1)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors: Mn2+
  • effectors:
  • protein partners:

Localization[edit source | edit]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • Internal Helix: 1
  • LocateP: N-terminally anchored (with CS)
    • Prediction by SwissProt Classification: Membrane
    • Pathway Prediction: Sec-(SPI)
    • Intracellular Possibility: 0.17
    • Signal Peptide Possibility: 0.5
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: GYVVARNL
  • SignalP: no predicted signal peptide
    • Ymax: 0.302
    • Ymax_pos: 36
    • Cmax: 0.303
    • Cmax_pos: 36
    • Smax: 0.476
    • Smax_pos: 33
    • Smean: 0.24
    • D: 0.278
  • predicted transmembrane helices (TMHMM): 1

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MNLLSLLLILLGIILGVVGGYVVARNLLLQKQSQARQTAEDIVNQAHKEADNIKKEKLLEAKEENQILREQTEAELRERRSELQRQETRLLQKEENLERKSDLLDKKDEILEQKESKIEEKQQQVDAKESSVQTLIMKHEQELERISGLTQEEAINEQLQRVEEELSQDIAVLVKEKEKEAKEKVDKTAKELLATAVQRLAADHTSESTVSVVNLPNDEMKGRIIGREGRNIRTLETLTGIDLIIDDTPEAVILSGFDPIRREIARTALVNLVSDGRIHPGRIEDMVEKARKEVDDIIREAGEQATFEVNAHNMHPDLVKIVGRLNYRTSYGQNVLKHSIEVAHLASMLAAELGEDETLAKRAGLLHDVGKAIDHEVEGSHVEIGVELAKKYGENETVINAIHSHHGDVEPTSIISILVAAADALSAARPGARKETLENYIRRLERLETLSESYDGVEKAFAIQAGREIRVIVSPEEIDDLKSYRLARDIKNQIEDELQYPGHIKVTVVRETRAVEYAK

Experimental data[edit source | edit]

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. Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
    Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
    BMC Genomics: 2009, 10;291
    [PubMed:19570206] [WorldCat.org] [DOI] (I e)
  2. Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  3. Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-3661
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  4. Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet.: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

Relevant publications[edit source | edit]

Chikara Kaito, Kenji Kurokawa, Yasuhiko Matsumoto, Yutaka Terao, Shigetada Kawabata, Shigeyuki Hamada, Kazuhisa Sekimizu
Silkworm pathogenic bacteria infection model for identification of novel virulence genes.
Mol. Microbiol.: 2005, 56(4);934-44
[PubMed:15853881] [WorldCat.org] [DOI] (P p)
Chikara Kaito, Daisuke Morishita, Yasuhiko Matsumoto, Kenji Kurokawa, Kazuhisa Sekimizu
Novel DNA binding protein SarZ contributes to virulence in Staphylococcus aureus.
Mol. Microbiol.: 2006, 62(6);1601-17
[PubMed:17087772] [WorldCat.org] [DOI] (P p)
Makiko Nagata, Chikara Kaito, Kazuhisa Sekimizu
Phosphodiesterase activity of CvfA is required for virulence in Staphylococcus aureus.
J. Biol. Chem.: 2008, 283(4);2176-84
[PubMed:17951247] [WorldCat.org] [DOI] (P p)
Gabriella Marincola, Tina Schäfer, Juliane Behler, Jörg Bernhardt, Knut Ohlsen, Christiane Goerke, Christiane Wolz
RNase Y of Staphylococcus aureus and its role in the activation of virulence genes.
Mol. Microbiol.: 2012, 85(5);817-32
[PubMed:22780584] [WorldCat.org] [DOI] (I p)