Literature DB >> 17572081

Ribozymes.

William G Scott1.   

Abstract

The structural molecular biology of ribozymes took another great leap forward during the past two years. Before ribozymes were discovered in the early 1980s, all enzymes were thought to be proteins. No detailed structural information on ribozymes became available until 1994. Now, within the past two years, near atomic resolution crystal structures are available for almost all of the known ribozymes. The latest additions include ribonuclease P, group I intron structures, the ribosome (the peptidyl transferase appears to be a ribozyme) and several smaller ribozymes, including a Diels-Alderase, the glmS ribozyme and a new hammerhead ribozyme structure that reconciles 12 years of discord. Although not all ribozymes are metalloenzymes, acid-base catalysis appears to be a universal property shared by all ribozymes as well as many of their protein cousins.

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Year:  2007        PMID: 17572081     DOI: 10.1016/j.sbi.2007.05.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  49 in total

1.  Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment.

Authors:  Kin-Yiu Wong; Hong Gu; Shuming Zhang; Joseph A Piccirilli; Michael E Harris; Darrin M York
Journal:  Angew Chem Int Ed Engl       Date:  2011-11-11       Impact factor: 15.336

2.  Computational prediction of efficient splice sites for trans-splicing ribozymes.

Authors:  Dario Meluzzi; Karen E Olson; Gregory F Dolan; Gaurav Arya; Ulrich F Müller
Journal:  RNA       Date:  2012-01-24       Impact factor: 4.942

3.  Multiscale methods for computational RNA enzymology.

Authors:  Maria T Panteva; Thakshila Dissanayake; Haoyuan Chen; Brian K Radak; Erich R Kuechler; George M Giambaşu; Tai-Sung Lee; Darrin M York
Journal:  Methods Enzymol       Date:  2015-01-22       Impact factor: 1.600

Review 4.  The peculiar interaction between mammalian prion protein and RNA.

Authors:  Mariana P B Gomes; Yraima Cordeiro; Jerson L Silva
Journal:  Prion       Date:  2008-04-11       Impact factor: 3.931

5.  The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a.

Authors:  M Duane Smith; Reza Mehdizadeh; Joan E Olive; Richard A Collins
Journal:  RNA       Date:  2008-08-12       Impact factor: 4.942

6.  Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.

Authors:  Tai-Sung Lee; George M Giambaşu; Carlos P Sosa; Monika Martick; William G Scott; Darrin M York
Journal:  J Mol Biol       Date:  2009-03-02       Impact factor: 5.469

7.  Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet.

Authors:  Jiro Kondo; Anne Catherine Dock-Bregeon; Dagmar K Willkomm; Roland K Hartmann; Eric Westhof
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2013-05-24

8.  Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.

Authors:  Tai-Sung Lee; Darrin M York
Journal:  J Am Chem Soc       Date:  2008-05-14       Impact factor: 15.419

9.  Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.

Authors:  Kin-Yiu Wong; Tai-Sung Lee; Darrin M York
Journal:  J Chem Theory Comput       Date:  2011-01-11       Impact factor: 6.006

10.  The shape-shifting quasispecies of RNA: one sequence, many functional folds.

Authors:  Matthew S Marek; Alexander Johnson-Buck; Nils G Walter
Journal:  Phys Chem Chem Phys       Date:  2011-05-20       Impact factor: 3.676

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