rnr [2019-08-30 17:39:45]

RNase R, required for protection against paraquate stress

locus: BSU_33610

pI: 5.70

mw: 88.56 kDa

protein length: 779 aa

gene length: 2340 bp

function: nonspecific degradation of rRNA

product: exoribonuclease RNase R (EC 3.1.-.-)

essential: no

synonyms: yvaJ

Genomic Context

categories

• [category|SW 2|Metabolism] → [category|SW 2.5|Nucleotide metabolism] → [category|SW 2.5.2|Biosynthesis/ acquisition of nucleotides] → [category|SW 2.5.2.5|Biosynthesis/ acquisition of nucleotides/ other]
• [category|SW 3|Information processing] → [category|SW 3.2|RNA synthesis and degradation] → [category|SW 3.2.4|RNases] → [category|SW 3.2.4.1|Exoribonucleases]
• [category|SW 4|Lifestyles] → [category|SW 4.3|Coping with stress] → [category|SW 4.3.8|Resistance against oxidative and electrophile stress]

Gene

Coordinates: 3,451,863 3,454,202

The protein

Catalyzed reaction/ biological activity

• 3'-5'-exoribonuclease
• Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates (according to UniProt)

Protein family

• RNR ribonuclease family (single member, according to UniProt)

[SW|Domains]

• [SW|S1 domain] (aa 625 ... 708) (according to the Interpro database)

Structure

• [PDB|5XGU] (from E. coli, 40% identity) [pubmed|29036353]

Expression and Regulation

Operons

• genes: [gene|D8851F453E5EF18D36F25834A8CB9C61EAF15E44|secG]-[gene|C0B6520E74CE9F7EE3DEC8C0D83E0770F241C4E8|yvaK]-[gene|0472A4346ADA1DC41C9D00E8F3222A0EBB76DFA8|rnr]-[gene|D19519B5A776D6E8EC2BFE7A7D67469CA0A6459A|smpB]-[gene|5C12BB19B975F7FEBCFA119DAC66338C20FCECFA|ssrA]
  description: [Pubmed|17369301]

  sigma factors

  • [protein|580011DE5DC40EC9E7E0512791D328FAA010DCB8|SigB]: sigma factor, [Pubmed|11544224], in [regulon|580011DE5DC40EC9E7E0512791D328FAA010DCB8|SigB regulon]

  regulation

  • ''[protein|search|yvaK]'': induced by stress ([protein|search|SigB]) [Pubmed|11544224]

• genes: [gene|C0B6520E74CE9F7EE3DEC8C0D83E0770F241C4E8|yvaK]-[gene|0472A4346ADA1DC41C9D00E8F3222A0EBB76DFA8|rnr]-[gene|D19519B5A776D6E8EC2BFE7A7D67469CA0A6459A|smpB]-[gene|5C12BB19B975F7FEBCFA119DAC66338C20FCECFA|ssrA]
  description: [Pubmed|17369301]

  regulation

  • ''[protein|search|yvaK]'': induced by stress ([protein|search|SigB]) [Pubmed|11544224]

Biological materials

Mutant

• MGNA-A495 (yvaJ::erm), available at the [https://shigen.nig.ac.jp/bsub/resource/strainGeneDisrupted/detail/495 NBRP B. subtilis, Japan]
• BKE33610 ([gene|0472A4346ADA1DC41C9D00E8F3222A0EBB76DFA8|rnr]::erm trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKE33610 BGSC], [Pubmed|28189581], upstream reverse: _UP1_TTCCATTATCCGACCTCCTG, downstream forward: _UP4_TAGCAGCTCAACCAGCAAAT
• BKK33610 ([gene|0472A4346ADA1DC41C9D00E8F3222A0EBB76DFA8|rnr]::kan trpC2) available at [http://www.bgsc.org/getdetail.php?bgscid=BKK33610 BGSC], [Pubmed|28189581], upstream reverse: _UP1_TTCCATTATCCGACCTCCTG, downstream forward: _UP4_TAGCAGCTCAACCAGCAAAT

labs

• [SW|David Bechhofer], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]

References

Reviews

• 25878039,30340785

Original publications

• 15805528,15805522,20360175,17369301,23529473,22582280,29873764,29036353