Ribozyme

The well-established natural ribozymes are the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud Satellite (VS), GlmS, twister, twister sister, pistol and hatchet ribozyme, which make up the category of small ribozymes, as well as the group I and II introns, the ribosome, spliceosome and RNase P, which are classified as large ribozymes (Discovery years means the year which corresponding ribozyme was found to be certified as a ribozyme.)

List of ribozymes

The small ribozymes also called nucleolytic ribozymes, which are a group of relatively small RNA species (the length is distributed around 50-150 nucleotides) that catalyze site‐specific cleavage reactions. In some ribozymes, the reverse reaction (ligation) can occur.

Sort table example

Name	Description	Discovery	Rfam-name	Rfam-ID
Small ribozymes
Hammerhead	The hammerhead ribozyme catalyzes the site‐specific self‐cleavage reaction and is named for the resemblance of early secondary structure diagrams to a hammerhead shark. It serves as a model system for research on the structure and properties of RNA and is used for targeted RNA cleavage experiments, some with proposed therapeutic applications.	1986	Hammerhead ribozyme (type III) Hammerhead ribozyme (type I) Hammerhead ribozyme HH9 Hammerhead ribozyme (type II) Hammerhead_HH10 RAGATH-1-hammerhead	RF00008 RF00163 RF02275 RF02276 RF02277 RF03152
HDV	The hepatitis delta virus (HDV) ribozyme is a viral-derived small ribozyme that catalyzes the site‐specific self‐cleavage reaction. These RNAs fold into a double-nested pseudoknot structure.	1988	Hepatitis delta virus ribozyme	RF00094
HDV-like ribozymes	The HDV-like ribozymes are a series of ribozymes structurally and biochemically related to HDV ribozymes. HDV-like ribozymes include the mammalian CPEB3 ribozyme, retrotransposons members and sequences from bacteria.	2006	HDV ribozyme from F. prausnitzii	RF02682
Hairpin	Hairpin ribozymes initially found in plant RNA viruses catalyze the site‐specific self‐cleavage reaction and consist of four stems in two general domains. The overall secondary structure of this RNA is hairpin-like and named the hairpin ribozyme.	1986	Hairpin ribozyme Hairpin ribozyme 1 from viruses-like metatranscriptomes Hairpin ribozyme 2 from viruses-like metatranscriptomes	RF00173 RF04190 RF04191
VS	The Varkud satellite (VS) ribozyme exists in the Neurospora mitochondria and performs site-specific scission of poly VS RNAs into linear monomers. The VS ribozyme is the largest known self-cleaving ribozyme.	1990	NA	NA
GlmS	The glmS riboswitch is a self‐cleavage ribozyme located in the 5' untranslated region of the glmS gene. The GlmS riboswitch can fold into two conformations depending on the presence or absence of glucosamine-6-phosphate. In one of these two conformations, the RNA cleaves itself, thereby inhibiting the synthesis of glucosamine-6-phosphate.	2004	GlmS glucosamine-6-phosphate activated ribozyme	RF00234
Twister	The twister ribozyme is a nucleolytic ribozyme. The nucleolytic activity of this ribozyme has been demonstrated both in vivo and in vitro and has one of the fastest catalytic rates of naturally occurring ribozymes with similar functions.	2014	Type-P1 twister ribozyme Type-P5 twister ribozyme Type-P3 twister ribozyme	RF03160 RF02684 RF03154
Twister-sister	The twister sister ribozyme (TS) is a nucleolytic ribozyme. It has a possible structural similarity to twister ribozymes. Some striking similarities were noted, but also surprising differences, such as the absence of the two pseudoknot interactions in the twister ribozyme.	2015	Twister_sister_ribozyme	RF02681
Hatchet	The hatchet ribozyme is a nucleolytic ribozyme.	2015	Hatchet ribozyme	RF02678
Pistol	The pistol ribozyme is a nucleolytic ribozyme. It was discovered by a bioinformatics strategy as an RNA Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH.	2015	Pistol ribozyme	RF02679
Hovlinc	Hovlinc (hominin vlincRNA-located) is a recently evolved class of ribozyme found in very long intergenic noncoding (vlinc) RNAs of humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes.	2021	Hovlinc ribozyme (hominin vlincRNA-located)	RF04188
LINE-1	The LongInterspersed Nuclear Element-1 (LINE-1) ribozyme is a nucleolytic ribozyme located in the 5′ untranslated region of a LINE-1 retrotransposon.	2006	NA	NA
CoTC ribozyme(Beta-globin co-transcriptional cleavage ribozyme)	Beta-globin co-transcriptional cleavage ribozyme (CoTC ribozyme) is considered to be involved in β- RNA self-cleavage activity in the 3' flanking region of the globin gene. However, these findings have not been independently confirmed, and subsequent analysis has failed to prove the activity of the ribozyme.	2004	Beta-globin co-transcriptional cleavage ribozyme	RF00621
Manganese dependent ribozyme in Vg1 mRNA	The Vg1 ribozyme is the smallest ribozyme to be identified which is a manganese-dependent ribozyme. The Vg1 ribozyme catalyzes a first-order reaction where its mechanism of cleavage is similar to the manganese ribozyme present in Tetrahymena group I introns.	2008	Manganese dependent ribozyme in Vg1 mRNA	RF01865
Large ribozymes
Group I self-splicing intron	Group I introns are the first ribozymes discovered in the 1980s. They can use exogenous guanosine as a cofactor to catalyze self-cleavage and exon ligation through sequential ester-transfer reactions. They are found in genes encoding rRNA, mRNA and tRNA in the nucleus, mitochondria and chloroplast in various organisms, from prokaryotes to eukaryotes.	1982	Group I catalytic intron	RF00028
Lariat capping ribozyme	The Lariat capping ribozyme is a ~180 nt ribozyme with an apparent resemblance to a group I ribozyme. It is found within a complex type of group I introns, also termed twin-ribozyme introns. It catalyses a branching reaction in which the 2'OH of an internal residue is involved in a nucleophilic attack at a nearby phosphodiester bond.	1995	GIR1 branching ribozyme	RF01807
A natural ribozyme with 3′,5′ RNA ligase activity	Group I intron from the cyanobacterium Anabaena sp. PCC 7120 catalyzes phosphodiester bond formation using a triphosphate on the 5′-terminal nucleotide, like protein polymerases and engineered ribozymes. This ribozyme forms a unique circular RNA that incorporates the exogenous guanosine cofactor added during self-splicing.	2009	NA	NA
Group II self-splicing intron	Group II introns are one of the largest ribozymes, with sequences ranging from 400 to 1000 nt in length. It is also the evolutionary ancestor of the Spliceosome. Group II introns can catalyze RNA self-splicing through an autocatalytic two-step reaction and mediate reverse-splicing. It plays an essential role in the metabolism of organisms and is now being developed as a tool in biotechnology and gene therapy.	1986	Group II catalytic intron	RF00029
RNase P	Ribonuclease (RNase) P is a ribozyme responsible for processing the 5′-leader of precursor transfer RNA (pre-tRNA) and is widely distributed in all three kingdoms of life: Archaea, Bacteria and Eucarya. RNase P is a ribonucleoprotein (RNP) complex consisting of catalytic RNA and one or more protein components.	1983	Nuclear RNase P Bacterial RNase P class A Bacterial RNase P class B Archaeal RNase P RNaseP truncated form RNase MRP	RF00009 RF00010 RF00011 RF00373 RF02357 RF00030
Ribosome	Ribosomes are the most critical macromolecules that widely exist in all three kingdoms of life, which catalyze the peptidyl transfer reaction to translate mRNA to proteins. It is the most abundant natural ribozyme with polymerase activity in nature.	2000	rRNA	NA
Spliceosome	The Spliceosome is a highly dynamic and heterogeneous metal ribozyme; During the splicing reaction, the dynamic spliceosome has an immobile core of about 20 protein and RNA components, which are organized around a conserved splicing active site. The divalent metal ions, coordinated by U6 small nuclear RNA (snRNA), catalyze the branching reaction and exon ligation.	2013	snRNA	NA