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NCBI: 10-JUN-2013

Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0540 [new locus tag: SACOL_RS02760 ]
  • pan locus tag?: SAUPAN002235000
  • symbol: SACOL0540
  • pan gene symbol?: yabJ
  • synonym:
  • product: endoribonuclease L-PSP

Genome View[edit | edit source]

Gene[edit | edit source]

General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0540 [new locus tag: SACOL_RS02760 ]
  • symbol: SACOL0540
  • product: endoribonuclease L-PSP
  • replicon: chromosome
  • strand: +
  • coordinates: 548804..549184
  • length: 381
  • essential: unknown other strains

Accession numbers[edit | edit source]

Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    ATGAAAATCATTAACACAACAAGATTACCGGAAGCACTTGGACCATATTCGCATGCAACA
    GTTGTGAATGGTATGGTTTATACTTCTGGTCAGATTCCATTGAATATTGATGGACATATC
    GTAAGCGCTGATGTTCAAGCACAGACAAAACAAGTTTTAGAAAATTTAAAGGTTGTTTTG
    GAAGAAGCAGGATCTGATTTGAATTCTGTTGCGAAAGCGACCATTTTCATTAAAGATATG
    AATGATTTCCAAAAAATAAATGAAGTGTATGGTCAATATTTTAATGAACACAAGCCAGCG
    CGTAGTTGTGTAGAGGTTGCGCGTTTGCCAAAAGATGTGAAAGTAGAAATTGAATTAGTA
    AGTAAAATTAAGGAATTATAA
    60
    120
    180
    240
    300
    360
    381

Protein[edit | edit source]

General[edit | edit source]

  • locus tag: SACOL0540 [new locus tag: SACOL_RS02760 ]
  • symbol: SACOL0540
  • description: endoribonuclease L-PSP
  • length: 126
  • theoretical pI: 6.25457
  • theoretical MW: 13996
  • GRAVY: -0.139683

Function[edit | edit source]

  • TIGRFAM:
    Cellular processes Cellular processes Other reactive intermediate/imine deaminase (TIGR00004; HMM-score: 169.2)
    and 2 more
    pyrimidine utilization protein C (TIGR03610; HMM-score: 99)
    amanitin/phalloidin family toxin (TIGR04309; HMM-score: 11.8)
  • TheSEED:  
    Nucleosides and Nucleotides Purines De Novo Purine Biosynthesis  YabJ, a purine regulatory protein and member of the highly conserved YjgF family
    and 2 more
    Protein Metabolism Protein biosynthesis Prolyl-tRNA synthetase associated editing enzymes  RidA/YER057c/UK114 superfamily protein
    RidA: all subgroups, 8100 genomes  RidA/YER057c/UK114 superfamily protein
  • PFAM:
    YjgF-like (CL0534) Ribonuc_L-PSP; Endoribonuclease L-PSP (PF01042; HMM-score: 148.3)
    and 2 more
    no clan defined Rab3-GTPase_cat; Rab3 GTPase-activating protein catalytic subunit (PF13890; HMM-score: 12.7)
    Eclosion; Eclosion hormone (PF04736; HMM-score: 12)

Structure, modifications & interactions[edit | edit source]

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

Localization[edit | edit source]

  • 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
    • SP(Sec/SPI): 0.03533
    • TAT(Tat/SPI): 0.001711
    • LIPO(Sec/SPII): 0.004131
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit | edit source]

Protein sequence[edit | edit source]

  • MKIINTTRLPEALGPYSHATVVNGMVYTSGQIPLNIDGHIVSADVQAQTKQVLENLKVVLEEAGSDLNSVAKATIFIKDMNDFQKINEVYGQYFNEHKPARSCVEVARLPKDVKVEIELVSKIKEL

Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
    experimental localization: Cytoplasmic [1] [2]
    quantitative data / protein copy number per cell: 143 [3]

Expression & Regulation[edit | edit source]

Operon[edit | edit source]

Regulation[edit | edit source]

  • regulator: RpoF* (activation) regulon
    RpoF(sigma factor)controlling a large regulon involved in stress/starvation response and adaptation [4]   other strains

Transcription pattern[edit | edit source]

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

Protein stability[edit | edit source]

  • half-life: 20.35 h [5]

Biological Material[edit | edit source]

Mutants[edit | edit source]

Expression vector[edit | edit source]

lacZ fusion[edit | edit source]

GFP fusion[edit | edit source]

two-hybrid system[edit | edit source]

FLAG-tag construct[edit | edit source]

Antibody[edit | edit source]

Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

Literature[edit | edit source]

References[edit | edit source]

  1. 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)
  2. 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)
  3. 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)
  4. Markus Bischoff, Paul Dunman, Jan Kormanec, Daphne Macapagal, Ellen Murphy, William Mounts, Brigitte Berger-Bächi, Steven Projan
    Microarray-based analysis of the Staphylococcus aureus sigmaB regulon.
    J Bacteriol: 2004, 186(13);4085-99
    [PubMed:15205410] [WorldCat.org] [DOI] (P p)
  5. 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 | edit source]