General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

Science. 2000 Feb 25;287(5457):1493-7. doi: 10.1126/science.287.5457.1493.

Abstract

Many protein enzymes use general acid-base catalysis as a way to increase reaction rates. The amino acid histidine is optimized for this function because it has a pK(a) (where K(a) is the acid dissociation constant) near physiological pH. The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a phosphodiester bond. Reactivity-pH profiles in monovalent or divalent cations, as well as distance to the leaving-group oxygen, implicate cytosine 75 (C75) of the ribozyme as the general acid and ribozyme-bound hydrated metal hydroxide as the general base in the self-cleavage reaction. Moreover, C75 has a pK(a) perturbed to neutrality, making it "histidine-like." Anticooperative interaction is observed between protonated C75 and a metal ion, which serves to modulate the pK(a) of C75. General acid-base catalysis expands the catalytic repertoire of RNA and may provide improved rate acceleration.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pairing
  • Binding Sites
  • Calcium / metabolism
  • Catalysis
  • Cobalt / metabolism
  • Crystallography, X-Ray
  • Hepatitis Delta Virus / chemistry*
  • Hepatitis Delta Virus / enzymology
  • Hydrogen Bonding
  • Hydrogen-Ion Concentration
  • Kinetics
  • Magnesium / metabolism
  • Metals / metabolism
  • Models, Chemical
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protons
  • RNA, Catalytic / chemistry
  • RNA, Catalytic / metabolism*
  • RNA, Viral / chemistry
  • RNA, Viral / metabolism
  • Static Electricity
  • Thermodynamics

Substances

  • Metals
  • Protons
  • RNA, Catalytic
  • RNA, Viral
  • cobalt ammonium complex
  • Cobalt
  • Magnesium
  • Calcium