Literature DB >> 8241158

Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism.

S C Dahm1, W B Derrick, O C Uhlenbeck.   

Abstract

The log of the rate of the chemical step of hammerhead cleavage in Mg2+ increases linearly with pH between pH 5.7 and 8.9. A slope of approximately 1 indicates that a single deprotonation is required for cleavage. Hammerhead pH-rate profiles with Ca2+, Mn2+, Co2+, and Cd2+ correlate well with the pKa's of these ions in water. This relationship between the pKa's and the pH-rate profile suggests that a metal hydroxide bound to the hammerhead RNA acts as the base in the cleavage mechanism.

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Year:  1993        PMID： 8241158     DOI： 10.1021/bi00211a013

Source DB:  PubMed          Journal:  Biochemistry        ISSN： 0006-2960            Impact factor:   3.162


  71 in total

1.  Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement.

Authors:  I H Shih; M D Been
Journal:  RNA       Date:  1999-09       Impact factor: 4.942

Review 2.  Recent advances in the elucidation of the mechanisms of action of ribozymes.

Authors:  Y Takagi; M Warashina; W J Stec; K Yoshinari; K Taira
Journal:  Nucleic Acids Res       Date:  2001-05-01       Impact factor: 16.971

3.  Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage.

Authors:  I H Shih ; M D Been
Journal:  Proc Natl Acad Sci U S A       Date:  2001-02-13       Impact factor: 11.205

4.  Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.

Authors:  R Pinard; K J Hampel; J E Heckman; D Lambert; P A Chan; F Major; J M Burke
Journal:  EMBO J       Date:  2001-11-15       Impact factor: 11.598

5.  Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.

Authors:  J L O'Rear; S Wang; A L Feig; L Beigelman; O C Uhlenbeck; D Herschlag
Journal:  RNA       Date:  2001-04       Impact factor: 4.942

6.  X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.

Authors:  V Tereshko; S T Wallace; N Usman; F E Wincott; M Egli
Journal:  RNA       Date:  2001-03       Impact factor: 4.942

7.  Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme.

Authors:  Jing-Min Zhou; De-Min Zhou; Yasuomi Takagi; Yasuhiro Kasai; Atsushi Inoue; Tadashi Baba; Kazunari Taira
Journal:  Nucleic Acids Res       Date:  2002-06-01       Impact factor: 16.971

8.  Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme.

Authors:  H Fauzi; J Kawakami; F Nishikawa; S Nishikawa
Journal:  Nucleic Acids Res       Date:  1997-08-01       Impact factor: 16.971

9.  Comparison of the specificities and catalytic activities of hammerhead ribozymes and DNA enzymes with respect to the cleavage of BCR-ABL chimeric L6 (b2a2) mRNA.

Authors:  T Kuwabara; M Warashina; T Tanabe; K Tani; S Asano; K Taira
Journal:  Nucleic Acids Res       Date:  1997-08-01       Impact factor: 16.971

10.  Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme.

Authors:  Hirohide Saito; Hiroaki Suga
Journal:  Nucleic Acids Res       Date:  2002-12-01       Impact factor: 16.971
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