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NCBI: 26-AUG-2013

Summary[edit source | edit]

  • organism: Staphylococcus aureus N315
  • locus tag: SA0735 [new locus tag: SA_RS04180 ]
  • pan locus tag?: SAUPAN002714000
  • symbol: rnr
  • pan gene symbol?: rnr
  • synonym:
  • product: ribonuclease R

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SA0735 [new locus tag: SA_RS04180 ]
  • symbol: rnr
  • product: ribonuclease R
  • replicon: chromosome
  • strand: +
  • coordinates: 840848..843220
  • length: 2373
  • essential: no 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
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    1981
    2041
    2101
    2161
    2221
    2281
    2341
    ATGAATTTAAAGCAATCAATAGAAGAGATTATTAATCAACCTGAATATGAACCTATGTCA
    GTGTCAGATTTTCAAGATGCATTAGGTTTAAGTAGTGCCGACTCATTTAGAGATTTAATT
    AAGGTGCTCGTAGAATTAGAACAATCAGGATTAATTGAACGTACAAAAACAGACAGATAT
    CAAAAAAAGCATAGTTCAAAAGGTCATTCAAAATTGATAAAGGGAACGTTAAGTCAAAAT
    AAAAAAGGCTTTGCATTCTTAAGACCTGAAGATGAGGATATGGAAGATATATTTATTCCC
    CCAACAAAAATTAATCGTGCCTTAGATGGAGATACTGTAATTGTAGAAATACATCAATCT
    AAAGGTGAACATAAAGGTAAAATTGAAGGGGAAGTTAAGTCGATTGAGAAGCATTCAGTA
    ACTCAAGTTGTTGGTACGTATAGTGAAGCTAGACATTTCGGATTTGTTATTCCAGATGAT
    AAACGTATTATGCAAGATATTTTCATTCCTAAAGGACAAAGTTTAGGTGCAGTAGATGGG
    CATAAGGTACTTGTTCAAATTACTAAATATGCTGATGGTTCAGATAATCCAGAAGGACAT
    ATTTCTGCTATTTTAGGACATAAAAATGATCCTGGCGTAGATATTTTATCTATTATCTAT
    CAACATGGCATAGAAATTGAATTTCCTGATGAAGTGTTACAAGAAGCTGAAGCAGTACCT
    GATCATATTGAAAATACTGAAATTAAAGGCCGTCATGATTTACGTGATGAATTGACAATC
    ACAATTGATGGTGCTGATGCTAAAGACTTAGATGACGCAATTAGTGTTAAAAAGTTAGCG
    AACGGTAATACGCAGTTGACTGTAAGTATTGCTGATGTCAGTTATTATGTAACTGAAGAT
    TCAGCTTTAGATAAAGAAGCTTATGATAGAGCGACAAGTGTATATCTTGTTGACCGTGTG
    ATTCCGATGATTCCACATCGATTAAGCAATGGTATTTGTTCATTAAATCCTCATGTTGAT
    CGTTTAACGTTAAGCTGTCGCATGGAAATCGATGCTAGTGGTCGCGTTGTTAAACATGAA
    ATTTTTGATAGTGTTATACATTCTGATTATCGAATGACGTATGATGCGGTAAATCAGATT
    ATTACTGAAAAGGATCCTAACATTCGCGAACAATATAAAGAAATTACGCCTATGTTAGAT
    TTAGCACAAGATTTATCTAATCGTTTGATTCAAATGAGAAAACGACGTGGTGAAATCGAT
    TTTGATATTAGTGAAGCAAAAGTATTAGTTAACGAAGTCGGTATACCAACAGATGTTCAA
    TTAAGACAACGTGGCGAGGGTGAACGTCTAATTGAATCATTTATGTTAATTGCAAATGAA
    ACAGTTGCTGAACATTTTAGTAAGTTAAATGTACCTTTTATTTACCGAGTGCATGAGCAA
    CCTAAATCAGATCGCTTAAGACAATTCTTTGATTTTATTACAAACTTTGGCATCATGATT
    AAGGGCACTGGCGAAGATATTCATCCAACAACACTTCAAAAGGTTCAAGAAGAAGTAGAA
    GGTCGACCTGAACAAATGGTCATTTCAACAATGATGTTACGTTCAATGCAACAAGCGCAT
    TATGATGATGTGAACTTGGGACATTTTGGCTTATCAGCTGAATATTATACGCATTTTACA
    TCACCAATTAGACGTTATCCTGATTTAACAGTTCATCGTTTAATCCGTAAGTATTTAATT
    GAGAAATCAATGGATAACAAAGAAGTGAAGCGTTGGGAAGACAAATTGCCTGAGTTAGCT
    GAACATACTTCTAAACGTGAACGTCGTGCTATTGAGGCAGAACGTGATACTGATGAATTG
    AAAAAAGCAGAATATATGATTCAACATATTGGTGATGAATTTGAAGGTATTGTCAGCTCA
    GTAGCTAACTTCGGTATGTTCATTGAATTGCCAAATACGATAGAAGGTATGGTTCATATT
    GCGAATATGACTGATGATTATTACCGTTTTGAAGAGCGTCAAATGGCATTAATTGGTGAG
    CGTCAAGCTAAAGTATTTAGAATTGGTGACACAGTTAAGGTTAAAGTGACGCATGTTGAT
    GTAGATGAACGATTAATTGATTTTCAAATTGTTGGAATGCCTTTACCTAAAAATGACCGC
    TCACAGCGACCAGCAAGAGGTAAAACGATTCAAGCTAAAACGCGTGGCAAATCTTTAGAT
    AAATCGAAATCTGATGATAAGGGTCGTAAGAAAAAAGGTAAGCAACGTAAAGGTAAAAAC
    CAACGTAATAATGATAAATCAGGTAATAGTAAGCATAAGCCATTTTATAAAGATAAAAGT
    GTGAAAAAGAAAGCACGTCGTAAGAAAAAATAA
    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
    2160
    2220
    2280
    2340
    2373

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SA0735 [new locus tag: SA_RS04180 ]
  • symbol: Rnr
  • description: ribonuclease R
  • length: 790
  • theoretical pI: 6.833
  • theoretical MW: 90418
  • GRAVY: -0.66481

Function[edit source | edit]

  • reaction:
  • TIGRFAM:
    Genetic information processingTranscriptionDegradation of RNAribonuclease R (TIGR02063; EC 3.1.-.-; HMM-score: 961.1)
    Genetic information processingTranscriptionDegradation of RNAVacB and RNase II family 3'-5' exoribonucleases (TIGR00358; EC 3.1.13.1; HMM-score: 731.7)
    Genetic information processingTranscriptionDegradation of RNAexoribonuclease II (TIGR02062; EC 3.1.13.1; HMM-score: 203.8)
    Genetic information processingTranscriptionDNA-dependent RNA polymeraseDNA-directed RNA polymerase (TIGR00448; EC 2.7.7.6; HMM-score: 40.7)
    Genetic information processingProtein synthesisRibosomal proteins: synthesis and modificationribosomal protein bS1 (TIGR00717; HMM-score: 30.4)
    Genetic information processingTranscriptionDegradation of RNApolyribonucleotide nucleotidyltransferase (TIGR03591; EC 2.7.7.8; HMM-score: 25.4)
    guanosine pentaphosphate synthetase I/polyribonucleotide nucleotidyltransferase (TIGR02696; EC 2.7.-.-,2.7.7.8; HMM-score: 14.7)
  • TheSEED:  
    RNA MetabolismRNA processing and modificationRNA processing and degradation, bacterial 3'-to-5' exoribonuclease RNase R 
  • PFAM:
    no clan definedRNB; RNB domain (PF00773; HMM-score: 370.2)
    OB (CL0021) OB_RNB; Ribonuclease B OB domain (PF08206; HMM-score: 101)
    S1; S1 RNA binding domain (PF00575; HMM-score: 61.5)
    CSD; 'Cold-shock' DNA-binding domain (PF00313; HMM-score: 16.7)
    Rho_RNA_bind; Rho termination factor, RNA-binding domain (PF07497; HMM-score: 15.9)
    no clan definedMacB_PCD; MacB-like periplasmic core domain (PF12704; HMM-score: 13.4)
    DUF2203; Uncharacterized conserved protein (DUF2203) (PF09969; HMM-score: 13.2)
    HTH (CL0123) MarR; MarR family (PF01047; HMM-score: 12.4)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:
    SA1305(hu)DNA-binding protein II  [1] (data from MRSA252)
    SA1504(infC)translation initiation factor IF-3  [1] (data from MRSA252)
    SA0038(mecA)penicillin binding protein 2 prime  [1] (data from MRSA252)
    SA2044(rplB)50S ribosomal protein L2  [1] (data from MRSA252)
    SA2047(rplC)50S ribosomal protein L3  [1] (data from MRSA252)
    SA2046(rplD)50S ribosomal protein L4  [1] (data from MRSA252)
    SA2035(rplE)50S ribosomal protein L5  [1] (data from MRSA252)
    SA2033(rplF)50S ribosomal protein L6  [1] (data from MRSA252)
    SA0497(rplJ)50S ribosomal protein L10  [1] (data from MRSA252)
    SA0498(rplL)50S ribosomal protein L7/L12  [1] (data from MRSA252)
    SA2029(rplO)50S ribosomal protein L15  [1] (data from MRSA252)
    SA2040(rplP)50S ribosomal protein L16  [1] (data from MRSA252)
    SA1084(rplS)50S ribosomal protein L19  [1] (data from MRSA252)
    SA1473(rplU)50S ribosomal protein L21  [1] (data from MRSA252)
    SA2042(rplV)50S ribosomal protein L22  [1] (data from MRSA252)
    SA2045(rplW)50S ribosomal protein L23  [1] (data from MRSA252)
    SAS052(rpsD)30S ribosomal protein S4  [1] (data from MRSA252)
    SA2031(rpsE)30S ribosomal protein S5  [1] (data from MRSA252)
    SA0352(rpsF)30S ribosomal protein S6  [1] (data from MRSA252)
    SA0504(rpsG)30S ribosomal protein S7  [1] (data from MRSA252)
    SA2016(rpsI)30S ribosomal protein S9  [1] (data from MRSA252)
    SA2024(rpsK)30S ribosomal protein S11  [1] (data from MRSA252)
    SA2038(rpsQ)30S ribosomal protein S17  [1] (data from MRSA252)
    SA2043(rpsS)30S ribosomal protein S19  [1] (data from MRSA252)
    SA0295hypothetical protein  [1] (data from MRSA252)
    SA0940hypothetical protein  [1] (data from MRSA252)
    SA1223hypothetical protein  [1] (data from MRSA252)
    SA1528hypothetical protein  [1] (data from MRSA252)
    SA1729nicotinate phosphoribosyltransferase  [1] (data from MRSA252)
    SA1885hypothetical protein  [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: 0.112
    • Ymax_pos: 62
    • Cmax: 0.116
    • Cmax_pos: 34
    • Smax: 0.146
    • Smax_pos: 54
    • Smean: 0.086
    • D: 0.102
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

  • GI: 15926457 NCBI
  • RefSeq: NP_373990 NCBI
  • UniProt:

Protein sequence[edit source | edit]

  • MNLKQSIEEIINQPEYEPMSVSDFQDALGLSSADSFRDLIKVLVELEQSGLIERTKTDRYQKKHSSKGHSKLIKGTLSQNKKGFAFLRPEDEDMEDIFIPPTKINRALDGDTVIVEIHQSKGEHKGKIEGEVKSIEKHSVTQVVGTYSEARHFGFVIPDDKRIMQDIFIPKGQSLGAVDGHKVLVQITKYADGSDNPEGHISAILGHKNDPGVDILSIIYQHGIEIEFPDEVLQEAEAVPDHIENTEIKGRHDLRDELTITIDGADAKDLDDAISVKKLANGNTQLTVSIADVSYYVTEDSALDKEAYDRATSVYLVDRVIPMIPHRLSNGICSLNPHVDRLTLSCRMEIDASGRVVKHEIFDSVIHSDYRMTYDAVNQIITEKDPNIREQYKEITPMLDLAQDLSNRLIQMRKRRGEIDFDISEAKVLVNEVGIPTDVQLRQRGEGERLIESFMLIANETVAEHFSKLNVPFIYRVHEQPKSDRLRQFFDFITNFGIMIKGTGEDIHPTTLQKVQEEVEGRPEQMVISTMMLRSMQQAHYDDVNLGHFGLSAEYYTHFTSPIRRYPDLTVHRLIRKYLIEKSMDNKEVKRWEDKLPELAEHTSKRERRAIEAERDTDELKKAEYMIQHIGDEFEGIVSSVANFGMFIELPNTIEGMVHIANMTDDYYRFEERQMALIGERQAKVFRIGDTVKVKVTHVDVDERLIDFQIVGMPLPKNDRSQRPARGKTIQAKTRGKSLDKSKSDDKGRKKKGKQRKGKNQRNNDKSGNSKHKPFYKDKSVKKKARRKKK

Experimental data[edit source | edit]

  • experimentally validated: no data available

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)

Relevant publications[edit source | edit]