PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 10-JUN-2013

⊟Summary

• organism: Staphylococcus aureus USA300_FPR3757
• locus tag: SAUSA300_1137 [new locus tag: SAUSA300_RS06155 ]
• pan locus tag^?: SAUPAN003536000
• symbol: rnhB
• pan gene symbol^?: rnhB
• synonym:
• product: ribonuclease HII

rnhB : ribonuclease H-II

• A crystal structure is available : 5Y9P

Staphylococci produce different paralogues of Ribonuclease H to introduce nicks in different RNA-DNA hybrid structures. Occasional misincorporation of single ribonucleotides in DNA duplex polymers can be managed by ribonucleotide excision repair. RNase H-II introduces a nick 5'- to a single ribonucleotide in a mostly DNA-DNA duplex. The nick allows DNA Pol I access to the ribonucleotide which it removes with its 5'→3' exonuclease activity and then fills in with a deoxyribonucleotide.

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SAUSA300_1137 [new locus tag: SAUSA300_RS06155 ]
• symbol: rnhB
• product: ribonuclease HII
• replicon: chromosome
• strand: +
• coordinates: 1245956..1246723
• length: 768
• essential: unknown other strains

⊟Accession numbers

• Gene ID: 3912975 NCBI
• RefSeq: YP_493834 NCBI
• BioCyc: see SAUSA300_RS06155
• MicrobesOnline: 1292652 MicrobesOnline

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

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  ATGACGCTAACAATTAAAGAAGTTACGCAGTTGATTAATGCGGTTAATACAATAGAAGAA
  TTAGAAAATCATGAATGCTTTTTAGATGAGCGAAAAGGTGTTCAAAATGCCATAGCTAGG
  CGCAGAAAAGCGTTAGAAAAAGAACAAGCTTTAAAAGAAAAGTATGTTGAAATGACTTAC
  TTTGAAAATGAAATATTAAAAGAGCATCCTAATGCTATTATTTGTGGGATTGATGAAGTT
  GGAAGAGGACCTTTAGCAGGTCCAGTCGTTGCATGCGCAACAATTTTAAATTCAAATCAC
  AATTATTTGGGCCTTGATGACTCGAAAAAAGTACCTGTTACGAAACGTCTAGAATTAAAT
  GAAGCACTAAAAAATGAAGTTACTGCTTTTGCATATGGGATCGCGACAGCTGAAGAAATA
  GATGAATTTAATATTTATAAAGCTACTCAAATCGCCATGCAGCGAGCTATTGATGGATTA
  TCAGTACAACCAACGCATTTATTGATAGACGCGATGACGCTTGATAATGCACTGCCTCAA
  GTATCTTTAATCAAGGGTGATGCAAGAAGTGTGTCCATTGCAGCTGCAAGTATCATGGCA
  AAGGTTTTTCGTGATGATTATATGACACAGTTATCTAAAGATTATCCTGAATATGGTTTT
  GAAAAAAACGCGGGTTACGGTACCAAACAACATTTACTAGCAATCGATGATATTGGCATT
  ATGAAAGAGCATAGAAAAAGCTTTGAACCTATAAAATCGTTACTGTAA
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⊟Protein

⊟General

• locus tag: SAUSA300_1137 [new locus tag: SAUSA300_RS06155 ]
• symbol: RnhB
• description: ribonuclease HII
• length: 255
• theoretical pI: 5.22942
• theoretical MW: 28512.5
• GRAVY: -0.247843

⊟Function

• reaction:
  EC 3.1.26.4?  ExPASy
  Ribonuclease H Endonucleolytic cleavage to 5'-phosphomonoester
• TIGRFAM:
  Genetic information processing DNA metabolism DNA replication, recombination, and repair ribonuclease HII (TIGR00729; EC 3.1.26.4; HMM-score: 74.5)
  and 1 more
  Genetic information processing DNA metabolism DNA replication, recombination, and repair ribonuclease HIII (TIGR00716; EC 3.1.26.4; HMM-score: 25.2)
• TheSEED  :
  • Ribonuclease HII (EC 3.1.26.4)
  RNA Metabolism RNA processing and modification Ribonuclease H  Ribonuclease HII (EC 3.1.26.4)
• PFAM:
  RNase_H (CL0219) RNase_HII; Ribonuclease HII (PF01351; HMM-score: 129.6)
  and 2 more
  no clan defined DUF3983; Protein of unknown function (DUF3983) (PF13137; HMM-score: 13.6)
  NTP_transf (CL0260) W02B3_4_N; W02B3.4-like, N-terminal domain (PF24413; HMM-score: 12.3)

⊟Structure, modifications & cofactors

• domains:
• modifications:
• cofactors: Mg²⁺, Mn²⁺
• effectors:

⊟Localization

• PSORTb: Cytoplasmic
  • Cytoplasmic Score: 7.5
  • Cytoplasmic Membrane Score: 1.15
  • Cellwall Score: 0.62
  • Extracellular Score: 0.73
  • Internal Helices: 0
• DeepLocPro: Cytoplasmic
  • Cytoplasmic Score: 0.9935
  • Cytoplasmic Membrane Score: 0.0001
  • Cell wall & surface Score: 0.0005
  • Extracellular Score: 0.0059
• 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): 0.00157
  • TAT(Tat/SPI): 0.000106
  • LIPO(Sec/SPII): 0.000209
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 87160122 NCBI
• RefSeq: YP_493834 NCBI
• UniProt: Q2FHJ4 UniProt

⊟Protein sequence

• MTLTIKEVTQLINAVNTIEELENHECFLDERKGVQNAIARRRKALEKEQALKEKYVEMTYFENEILKEHPNAIICGIDEVGRGPLAGPVVACATILNSNHNYLGLDDSKKVPVTKRLELNEALKNEVTAFAYGIATAEEIDEFNIYKATQIAMQRAIDGLSVQPTHLLIDAMTLDNALPQVSLIKGDARSVSIAAASIMAKVFRDDYMTQLSKDYPEYGFEKNAGYGTKQHLLAIDDIGIMKEHRKSFEPIKSLL

⊟Experimental data

• experimentally validated: data available for COL, NCTC8325
• protein localization: data available for COL
• quantitative data / protein copy number per cell:
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: rbgA > rnhB

⊟Regulation

• regulator:

⊟Transcription pattern

• S.aureus Expression Data Browser: data available for NCTC8325

⊟Protein synthesis (provided by Aureolib)

• Aureolib: no data available

⊟Protein stability

• half-life: no data available

⊟Biological Material

⊟Mutants

⊟Expression vector

⊟lacZ fusion

⊟GFP fusion

⊟two-hybrid system

⊟FLAG-tag construct

⊟Antibody

⊟Other Information

You are kindly invited to share additional interesting facts.

⊟Literature

⊟References

⊟Relevant publications