Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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RIBOc Ribonuclease III family

SMART accession number:	SM00535
Description:
Interpro abstract (IPR000999):	Prokaryotic ribonuclease III (EC 3.1.26.3) (gene rnc) [(PUBMED:3903434)] is an enzyme that digests double-stranded RNA. It is involved in the processing of ribosomal RNA precursors and of some mRNAs. RNase III is evolutionary related to a number of proteins including [(PUBMED:9241229)]: Saccharomyces cerevisiae (Baker's yeast) protein pac1, a ribonuclease that probably inhibits mating and meiosis by degrading a specific mRNA required for sexual development yeast ribonuclease III (gene RNT1), a dsRNA-specific nuclease that cleaves eukaryotic preribosomal RNA at various sites Caenorhabditis elegans hypothetical protein F26E4.13 Paramecium bursaria Chlorella virus 1 (PBCV-1) 1 protein A464R Synechocystis sp. (strain PCC 6803) hypothetical protein slr0346 yeast hypothetical protein SpAC8A4.08c, a protein with a N-terminal helicase domain and a C-terminal RNase III domain C. elegans hypothetical protein K12H4.8, a protein with the same structure as SpAC8A4.08c
GO process:	RNA processing (GO:0006396)
GO function:	RNA binding (GO:0003723), ribonuclease III activity (GO:0004525)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 2906 RIBOc domains in 2557 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a RIBOc domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with RIBOc domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Mian IS
  • Comparative sequence analysis of ribonucleases HII, III, II PH and D.
  • Nucleic Acids Res. 1997; 25: 3187-95
  • Display abstract

  • Escherichia coli ribonucleases (RNases) HII, III, II, PH and D have been used to characterise new and known viral, bacterial, archaeal and eucaryotic sequences similar to these endo- (HII and III) and exoribonucleases (II, PH and D). Statistical models, hidden Markov models (HMMs), were created for the RNase HII, III, II and PH and D families as well as a double-stranded RNA binding domain present in RNase III. Results suggest that the RNase D family, which includes Werner syndrome protein and the 100 kDa antigenic component of the human polymyositis scleroderma (PMSCL) autoantigen, is a 3'-->5' exoribonuclease structurally and functionally related to the 3'-->5' exodeoxyribonuclease domain of DNA polymerases. Polynucleotide phosphorylases and the RNase PH family, which includes the 75 kDa PMSCL autoantigen, possess a common domain suggesting similar structures and mechanisms of action for these 3'-->5' phosphorolytic enzymes. Examination of HMM-generated multiple sequences alignments for each family suggest amino acids that may be important for their structure, substrate binding and/or catalysis.

  • Nashimoto H, Uchida H
  • DNA sequencing of the Escherichia coli ribonuclease III gene and its mutations.
  • Mol Gen Genet. 1985; 201: 25-9
  • Display abstract

  • A 0.7 kb DNA fragment of the Escherichia coli K12 chromosome was shown to contain the structural gene for RNAse III (rnc). The DNA sequence of the gene was determined and its alteration in an RNAse III defective mutant, AB301-105, was identified. DNA sequence analysis also showed that a secondary-site suppressor of a temperature-sensitive mutation in the E. coli ribosomal protein gene, rpsL, occurred within the rnc gene, providing genetic evidence for the interaction of ribosomal proteins with RNAse III, which in turn acts on the nascent ribosomal RNA during assembly of ribosomes in E. coli.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 40.00 map03010 Ribosome 20.00 map00500 Starch and sucrose metabolism 20.00 map00790 Folate biosynthesis 20.00 map00230 Purine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with RIBOc domain which could be assigned to a KEGG orthologous group, and not all proteins containing RIBOc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of RIBOc domains in PDB

  PDB code	Main view	Title
  1i4s		Crystal structure of rnase iii endonuclease domain from aquifex aeolicus at 2.15 angstrom resolution
  1jfz		Crystal structure of mn(ii)-complex of rnase iii endonuclease domain from aquifex aeolicus at 2.10 angstrom resolution
  1o0w		Crystal structure of ribonuclease iii (tm1102) from thermotoga maritima at 2.0 a resolution
  1rc5		Crystal structure of mg(ii)-complex of rnase iii endonuclease domain from aquifex aeolicus at 2.30 angstrom resolution
  1rc7		Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with ds-rna at 2.15 angstrom resolution
  1u61		Crystal structure of putative ribonuclease iii from bacillus cereus
  1yyk		Crystal structure of rnase iii from aquifex aeolicus complexed with double-stranded rna at 2.5-angstrom resolution
  1yyo		Crystal structure of rnase iii mutant e110k from aquifex aeolicus complexed with double-stranded rna at 2.9- angstrom resolution
  1yyw		Crystal structure of rnase iii from aquifex aeolicus complexed with double stranded rna at 2.8-angstrom resolution
  1yz9		Crystal structure of rnase iii mutant e110q from aquifex aeolicus complexed with double stranded rna at 2.1- angstrom resolution
  2a11		Crystal structure of nuclease domain of ribonuclase iii from mycobacterium tuberculosis
  2eb1		Crystal structure of the c-terminal rnase iii domain of human dicer
  2ez6		Crystal structure of aquifex aeolicus rnase iii (d44n) complexed with product of double-stranded rna processing
  2ffl		Crystal structure of dicer from giardia intestinalis
  2gsl		X-ray crystal structure of protein fn1578 from fusobacterium nucleatum. northeast structural genomics consortium target nr1.
  2nue		Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 2.9-angstrom resolution
  2nuf		Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 2.5-angstrom resolution
  2nug		Crystal structure of rnase iii from aquifex aeolicus complexed with ds-rna at 1.7-angstrom resolution
  2qvw		Structure of giardia dicer refined against twinned data
  3c4b		Structure of rnaseiiib and dsrna binding domains of mouse dicer
  3c4t		Structure of rnaseiiib and dsrna binding domains of mouse dicer

• Links (links to other resources describing this domain)

• PFAM	Ribonuclease_3
  INTERPRO	IPR000999
  PROSITE	RIBONUCLEASE_III

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