Science. 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10.

Transition state stabilization by a catalytic RNA.

Rupert PB, Massey AP, Sigurdsson ST, Ferré-D'Amaré AR.

Source

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

Abstract

The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.

PMID:: 12376595; [PubMed - indexed for MEDLINE]

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

OXYGEN - HSDB

Supplemental Content

Save items

Related citations in PubMed

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. [RNA. 2007]
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
Torelli AT, Krucinska J, Wedekind JE. RNA. 2007 Jul; 13(7):1052-70. Epub 2007 May 8.
Review Catalytic strategies of self-cleaving ribozymes. [Acc Chem Res. 2008]
Review Catalytic strategies of self-cleaving ribozymes.
Cochrane JC, Strobel SA. Acc Chem Res. 2008 Aug; 41(8):1027-35. Epub 2008 Jul 25.
The structural basis of ribozyme-catalyzed RNA assembly. [Science. 2007]
The structural basis of ribozyme-catalyzed RNA assembly.
Robertson MP, Scott WG. Science. 2007 Mar 16; 315(5818):1549-53.
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. [Science. 2006]
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
Klein DJ, Ferré-D'Amaré AR. Science. 2006 Sep 22; 313(5794):1752-6.
Review Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. [Biochemistry. 2003]
Review Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme.
Bevilacqua PC. Biochemistry. 2003 Mar 4; 42(8):2259-65.

See reviews... See all...

Cited by 54 PubMed Central articles

Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules. [Philos Trans R Soc Lond B Biol...]
Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules.
Ferré-D'Amaré AR. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27; 366(1580):2942-8.
The chemical versatility of RNA. [Philos Trans R Soc Lond B Biol...]
The chemical versatility of RNA.
Hiller DA, Strobel SA. Philos Trans R Soc Lond B Biol Sci. 2011 Oct 27; 366(1580):2929-35.
The structural basis of RNA-catalyzed RNA polymerization. [Nat Struct Mol Biol. 2011]
The structural basis of RNA-catalyzed RNA polymerization.
Shechner DM, Bartel DP. Nat Struct Mol Biol. 2011 Aug 21; 18(9):1036-42. Epub 2011 Aug 21.

See all...

Structures reported by this article

Crystal Structure Of A Hairpin Ribozyme In The Catalytically-Active Conformationÿ

PDB: 1M5K

Source: synthetic construct, Homo sapiens

Method: X-Ray Diffraction

Resolution: 2.4 Å

See all 4 structures...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Nucleotide
Primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Taxonomy via GenBank
Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).
Protein
Protein translation features of primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
Structure
Three-dimensional structure records in the NCBI Structure database for data reported in the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Transition state stabilization by a catalytic RNA.
Transition state stabilization by a catalytic RNA.
Science. 2002 Nov 15 ;298(5597):1421-4. Epub 2002 Oct 10 .

PubMed
Bupropion SR vs. placebo for weight loss in obese patients with depressive sympt...
Bupropion SR vs. placebo for weight loss in obese patients with depressive symptoms.
Obes Res. 2002 Oct ;10(10):1049-56.

PubMed
Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear...
Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing.
Mol Cell Proteomics. 2002 Aug ;1(8):598-610.

PubMed
Effects of limited work hours on surgical training.
Effects of limited work hours on surgical training.
J Am Coll Surg. 2002 Oct ;195(4):531-8.

PubMed
Biochemical and structural changes in RBCs stored with different plasticizers: t...
Biochemical and structural changes in RBCs stored with different plasticizers: the role of hexanol.
Transfusion. 2002 Jul ;42(7):830-5.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to:

Transition state stabilization by a catalytic RNA.

Source

Abstract

Publication Types, MeSH Terms, Substances, Secondary Source ID, Grant Support

Publication Types

MeSH Terms

Substances

Secondary Source ID

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases

Supplemental Content

Save items

Related citations in PubMed

Cited by 54 PubMed Central articles

Structures reported by this article

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information