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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Escherichia coli K-12 substr. MG1655 Compound: 5S ribosomal RNA (rrfA)

Synonyms: rrfA

Superclasses: 5S rRNA

Component of: 50S ribosomal subunit

Summary:
The 5S and 23S rRNAs are the RNA components of the large subunit (50S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrnA, rrnB, rrnC, rrnD, rrnE, rrnG, and rrnH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrnD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes. Regarding nomenclature, "rrs" genes encode 16S rRNAs, "rrl" genes encode 23S rRNAs, and "rrf" genes encode 5S rRNAs [Neidhardt96].

The sequence and structure of the 5S rRNA has been described, and the relationship of the 5S rRNA to ribosome assembly, structure, and function has been characterized. Interactions between the 5S rRNA and 23S rRNA as well as ribosomal proteins have been described. Mutations in 5S rRNA have been analyzed, and the post-transcriptional processing of the 5S rRNA has been characterized.

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03a].

Reviews: [Lind, Azad79, Tanaka85, Nowotny88, Moore88, Vester88, Goringer88, Srivastava91, Barciszewska96, Barciszewska97].

Gene: rrfA Accession Numbers: EG30070 (EcoCyc), b3855, ECK3847

Sequence Length: 39 AAs

Unification Links: EcoliWiki:b3855

Reactions known to consume the compound:

Not in pathways:
rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine

Reactions known to produce the compound:

Not in pathways:
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA


an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]


rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Enzymes inhibited by 5S ribosomal RNA (rrfA), sorted by the type of inhibition, are:

Inhibitor (Mechanism unknown) of: 3'-nucleotidase [Anraku64]

Gene-Reaction Schematic: ?

MultiFun Terms: cell structure ribosomes
information transfer protein related translation
information transfer RNA related rRNA, stable RNA


References

Anraku64: Anraku Y (1964). "A new cyclic phosphodiesterase having a 3'-nucleotidase activity from Escherichia coli B. II. Further studies on substrate specificity and mode of action of the enzyme." J Biol Chem 239;3420-4. PMID: 14245397

Azad79: Azad AA (1979). "Intermolecular base-paired interaction between complementary sequences present near the 3' ends of 5S rRNA and 18S (16S) rRNA might be involved in the reversible association of ribosomal subunits." Nucleic Acids Res 7(7);1913-29. PMID: 94160

Barciszewska96: Barciszewska MZ, Erdmann VA, Barciszewski J (1996). "Ribosomal 5S RNA: tertiary structure and interactions with proteins." Biol Rev Camb Philos Soc 71(1);1-25. PMID: 8603119

Barciszewska97: Barciszewska MZ (1997). "[RNA tectonics]." Postepy Biochem 43(4);267-74. PMID: 9572078

Goringer88: Goringer HU, Wagner R (1988). "5S RNA structure and function." Methods Enzymol 164;721-47. PMID: 3071691

Lind: Lind AIa, Villems RL, Uuskiula LS "[5S RNA: structure and function]." Usp Sovrem Biol 86(1);3-18. PMID: 152015

Moore88: Moore PB, Abo S, Freeborn B, Gewirth DT, Leontis NB, Sun G (1988). "Preparation of 5S RNA-related materials for nuclear magnetic resonance and crystallography studies." Methods Enzymol 164;158-74. PMID: 3071660

Neidhardt96: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low Jr KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE "Escherichia coli and Salmonella, Cellular and Molecular Biology, Second Edition." American Society for Microbiology, Washington, D.C., 1996.

Nowotny88: Nowotny P, Nowotny V, Voss H, Nierhaus KH (1988). "Preparation and activity measurements of deuterated 50S subunits for neutron-scattering analysis." Methods Enzymol 164;131-47. PMID: 3071658

Schneider03a: Schneider DA, Ross W, Gourse RL (2003). "Control of rRNA expression in Escherichia coli." Curr Opin Microbiol 6(2);151-6. PMID: 12732305

Srivastava91: Srivastava AK, Schlessinger D (1991). "Structure and organization of ribosomal DNA." Biochimie 73(6);631-8. PMID: 1764510

Tanaka85: Tanaka T, Ogata K (1985). "[The structure and the evolution of the 5S RNA protein complex]." Seikagaku 57(11);1531-4. PMID: 3913708

Vester88: Vester B, Egebjerg J, Garrett R, Christiansen J (1988). "Primer-directed deletions in 5S ribosomal RNA." Methods Enzymol 164;710-21. PMID: 3071690


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc14.