Exoribonuclease

Reaction diagrams for both hydrolytic (left) and phosphorolytic (right) 3'-5' exoribonuclease degradation of RNA.

An exoribonuclease is an exonuclease ribonuclease, which are enzymes that degrade RNA by removing terminal nucleotides from either the 5' end or the 3' end of the RNA molecule. Enzymes that remove nucleotides from the 5' end are called 5'-3' exoribonucleases, and enzymes that remove nucleotides from the 3' end are called 3'-5' exoribonucleases.

Exoribonucleases can use either water to cleave the nucleotide-nucleotide bond (which is called hydrolytic activity) or inorganic phosphate (which is called phosphorolytic activity). Hydrolytic exoribonucleases are classified under EC number 3.1 and phosphorolytic exoribonucleases under EC number 2.7.7. As the phosphorolytic enzymes use inorganic phosphate to cleave bonds they release nucleotide disphosphates), whereas the hydrolytic enzymes (which use water) release nucleotide monosphosphates).

Exoribonucleases exist in all kingdoms of life, the bacteria, archaea, and eukaryotes. Exoribonucleases are involved in the degradation of many different RNA species, including messenger RNA, transfer RNA, ribosomal RNA and miRNA. Exoribonucleases can be single proteins (such as RNase D or RNase PH) but also can be complexes of multiple proteins, such as the exosome complex (in which four of the major exoribonuclease families are represented).

Major families

Family	Example members	Distribution	Catalytic activity
RNR	RNase R	Most bacteria, all eukaryotes	3'-5' hydrolytic
	RNase II
	Rrp44
DEDD	RNase D	Certain bacteria, all eukaryotes	3'-5' hydrolytic
	RNase T
	PM/Scl-100
	Oligoribonuclease
RBN	RNase BN	Certain bacteria	3'-5' hydrolytic
PDX	PNPase	All kingdoms	3'-5' phosphorolytic
	PM/Scl-75
	RNase PH
RRP4	Rrp4	All eukaryotes, most archaea	3'-5' hydrolytic
5PX	Exoribonuclease I	All eukaryotes	5'-3' hydrolytic
5PX	Exoribonuclease II	All eukaryotes	5'-3' hydrolytic

References

Zuo Y, Deutscher MP. (2001). "Exoribonuclease superfamilies: structural analysis and phylogenetic distribution". Nucleic Acids Res. 29 (5): 1017–26. doi:10.1093/nar/29.5.1017. PMC 56904. PMID 11222749.

External links

Exoribonucleases at the US National Library of Medicine Medical Subject Headings (MeSH)

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic
ester hydrolases

Lipase

Phospholipase
- A1
- A2
- B

3.1.2: Thioesterase

3.1.3: Phosphatase

3.1.4: Phosphodiesterase

3.1.6: Sulfatase

Nuclease (includes
deoxyribonuclease and
ribonuclease)

3.1.11-16: Exonuclease

Exodeoxyribonuclease	RecBCD

Exoribonuclease	Oligonucleotidase

3.1.21-31: Endonuclease

Endodeoxyribonuclease	Deoxyribonuclease I Deoxyribonuclease II Deoxyribonuclease IV Restriction enzyme UvrABC endonuclease

Endoribonuclease	RNase III RNase H 1 2A 2B 2C RNase P RNase A 1 2 3 4/5 RNase T1 RNA-induced silencing complex

either deoxy- or ribo-	Aspergillus nuclease S1 Micrococcal nuclease

Transferases: phosphorus-containing groups (EC 2.7)

2.7.1-2.7.4:
phosphotransferase/kinase
(PO₄)

2.7.1: OH acceptor	Hexo- Gluco- Fructo- Hepatic Galacto- Phosphofructo- 1 Liver Muscle Platelet 2 Riboflavin Shikimate Thymidine ADP-thymidine NAD⁺ Glycerol Pantothenate Mevalonate Pyruvate Deoxycytidine PFP Diacylglycerol Phosphoinositide 3 Class I PI 3 Class II PI 3 Sphingosine Glucose-1,6-bisphosphate synthase

2.7.2: COOH acceptor	Phosphoglycerate Aspartate kinase

2.7.3: N acceptor	Creatine

2.7.4: PO₄ acceptor	Phosphomevalonate Adenylate Nucleoside-diphosphate Uridylate Guanylate Thiamine-diphosphate

2.7.6: diphosphotransferase
(P₂O₇)

2.7.7: nucleotidyltransferase
(PO₄-nucleoside)

Polymerase

DNA polymerase	DNA-directed DNA polymerase I II III IV V RNA-directed DNA polymerase Reverse transcriptase Telomerase DNA nucleotidylexotransferase/Terminal deoxynucleotidyl transferase

RNA nucleotidyltransferase	RNA polymerase/DNA-directed RNA polymerase RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase IV Primase RNA-dependent RNA polymerase PNPase

Phosphorolytic
3' to 5' exoribonuclease

Nucleotidyltransferase

Guanylyltransferase

mRNA capping enzyme

Other

2.7.8: miscellaneous

Phosphatidyltransferases	CDP-diacylglycerol—glycerol-3-phosphate 3-phosphatidyltransferase CDP-diacylglycerol—serine O-phosphatidyltransferase CDP-diacylglycerol—inositol 3-phosphatidyltransferase CDP-diacylglycerol—choline O-phosphatidyltransferase

Glycosyl-1-phosphotransferase	N-acetylglucosamine-1-phosphate transferase

2.7.10-2.7.13: protein kinase
(PO₄; protein acceptor)

2.7.10: protein-tyrosine	see tyrosine kinases

2.7.11: protein-serine/threonine	see serine/threonine-specific protein kinases

2.7.12: protein-dual-specificity	see serine/threonine-specific protein kinases

2.7.13: protein-histidine	Protein-histidine pros-kinase Protein-histidine tele-kinase Histidine kinase

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Exoribonuclease

Major families

See also

References

External links