Catalytic strategies of the hepatitis delta virus ribozymes.
The hepatitis delta virus (HDV) ribozymes are self-cleaving RNA sequences critical to the replication of a small RNA genome. A recently determined crystal structure together with biochemical and biophysical studies provides new insight into the possible catalytic mechanism of these ribozymes. The HDV ribozymes are examples of naturally occurring small ribozymes that catalyze cleavage of the RNA backbone with a rate enhancement of 10(6)- to 10(7)-fold over the uncatalyzed rate. To achieve this level of rate enhancement, the HDV ribozymes have been proposed to employ several catalytic strategies that include the use of metal ions, intrinsic binding energy, and a novel example of general acid-base catalysis with a cytosine side chain acting as a proton donor or acceptor.
Shih
I-hung
IH
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA. been@biochem.duke.edu.
Been
Michael D
MD
D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D002413:Cations, Divalent / Q000378:metabolism; D003698:Hepatitis Delta Virus / Q000201:enzymology* / Q000235:genetics; D008670:Metals / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017510:Protein Folding; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D002413:Cations, Divalent; D008670:Metals; D016337:RNA, Catalytic; D012367:RNA, Viral; D014764:Viral Proteins