Rfam ID: RF00622

click into different sections:


  • 2006 A HDV-like sequence in the human CPEB3 gene[1]

  • 2009 HDV-like ribozymes in other species[2]

  • 2010 A HDV-like ribozyme encoded by R2 retrotransposons[3]

  • 2011 A HDV-like ribozyme in L1Tc mRNA[4]

  • 2011 More retrotransposons encode HDV-like ribozymes[6]

  • 2014 NMR solution structure of CPEB3 ribozyme's P4 domain[7]

  • 2015 HDV ribozyme variants in bacterial metagenomes and fungal genomes[8]

  • 2016 NMR studies confirm secondary structure and Mg2+ location in CPEB3 ribozyme [9]

  • 2017 More HDV ribozyme variants in fungi[10]

  • 2021 The functional conservation of CPEB3 ribozyme in mammalian evolution[11]


The HDV-like ribozymes are many ribozymes structurally and biochemically related to HDV ribozymes. HDV-like ribozymes include the mammalian CPEB3 ribozyme, retrotransposons members and sequences from bacteria and other species. Genomic mapping of these RNAs suggested several biological roles, one of which is the degradation or processing of pre-mRNA.

Structure and mechanism

2D representation

Secondary structure depictions of the human CPEB3 ribozyme with the scissile phosphates (blue). The human CPEB3 ribozymes act with the direct involvement of metal ions shown by green spheres with octahedral coordination of red water molecules of hydration.



[1] A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene.
Salehi-Ashtiani, K., A. Luptak, A. Litovchick and J. W. zostak.
Science 313 (5794): 1788-92.(2006)

[2] Widespread occurrence of self-cleaving ribozymes.
Webb, C. H., N. J. Riccitelli, D. J. Ruminski and A. Luptak
Science 326 (5955): 953.(2009)

[3] R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript.
Eickbush, D. G. and T. H. Eickbush
Mol Cell Biol 30 (13): 3142-50.(2010)

[4] Identification of an hepatitis delta virus-like ribozyme at the mRNA 5'-end of the L1Tc retrotransposon from Trypanosoma cruzi.
Sanchez-Luque, F. J., M. C. Lopez, F. Macias, C. Alonso and M. C. Thomas
Nucleic Acids Res 39 (18): 8065-77.(2011)

[5] HDV-like self-cleaving ribozymes.
Webb, C. H. and A. Luptak
RNA Biol 8 (5): 719-27.(2011)

[6] Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes.
Ruminski, D. J., C. T. Webb, N. J. Riccitelli and A. Luptak.
J Biol Chem 286 (48): 41286-41295.(2011)

[7] Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain.
Skilandat, M., M. Rowinska-Zyrek and R. K. Sigel
J Biol Inorg Chem 19 (6): 903-12.(2014)

[8] New classes of self-cleaving ribozymes revealed by comparative genomics analysis.
Weinberg, Z., P. B. Kim, T. H. Chen, S. Li, K. A. Harris, C. E. Lunse and R. R. Breaker
Nat Chem Biol 11 (8): 606-10.(2015)

[9] Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.
Skilandat, M., M. Rowinska-Zyrek and R. K. Sigel
RNA 22 (5): 750-63.(2016)

[10] Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics.
Li, S. and R. R. Breaker
BMC Genomics 18 (1): 785.(2017)

[11] Experimental Resurrection of Ancestral Mammalian CPEB3 Ribozymes Reveals Deep Functional Conservation.
Bendixsen, D. P., T. B. Pollock, G. Peri and E. J. Hayden
Mol Biol Evol 38 (7): 2843-2853.(2021)