Ligand Requirements for glmS Ribozyme Self-Cleavage

McCarthy, Tom J.; Plog, Melissa A.; Floy, Shennen A.; Jansen, Joshua A; Soukup, Juliane K.; Soukup, Garrett A.

doi:10.1016/j.chembiol.2006.06.003

Cited by 44 publications

(105 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…All the nucleolytic ribozymes seem to employ general acid-base catalysis. In addition to the nucleobases, this class of ribozyme has evolved the use of bound hydrated metal ions (2) and glucosamine-6-phosphate (32,33). All these alternatives have a pK a far from neutrality.…”

Section: Discussionmentioning

confidence: 99%

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

Wilson

Lü

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

120

View full text Add to dashboard Cite

Existing evidence suggests that the Varkud satellite (VS) ribozyme accelerates the cleavage of a specific phosphodiester bond using general acid-base catalysis. The key functionalities are the nucleobases of adenine 756 in helix VI of the ribozyme, and guanine 638 in the substrate stem loop. This results in a bell-shaped dependence of reaction rate on pH, corresponding to groups with pK a ¼ 5.2 and 8.4. However, it is not possible from those data to determine which nucleobase is the acid, and which the base. We have therefore made substrates in which the 5′ oxygen of the scissile phosphate is replaced by sulfur. This labilizes the leaving group, removing the requirement for general acid catalysis. This substitution restores full activity to the highly impaired A756G ribozyme, consistent with general acid catalysis by A756 in the unmodified ribozyme. The pH dependence of the cleavage of the phosphorothiolatemodified substrates is consistent with general base catalysis by nucleobase at position 638. We conclude that cleavage of the substrate by the VS ribozyme is catalyzed by deprotonation of the 2′-O nucleophile by G638 and protonation of the 5′-O leaving group by A756. 5′-phosphorothiolate | RNA catalysis | nucleolytic ribozymes | catalytic mechanism R ibozyme-mediated catalysis is important for both RNA splicing and translation (1), yet its chemical origins are incompletely understood. The nucleolytic ribozymes bring about the site-specific cleavage or ligation of RNA, with an acceleration of a millionfold or greater. The intensively studied protein RNase A catalyses an identical cleavage reaction, and much evidence supports the hypothesis that each of these phosphoryl transfer reactions is subject to general acid-base catalysis. This mechanism requires a general base to deprotonate the attacking nucleophile, and a general acid to protonate the oxyanion leaving group (Fig. 1).The most common chemical entities implicated in RNA catalysis by the nucleolytic ribozymes are the nucleobases (2). Guanine appears to play a catalytic role in the hairpin, hammerhead, GlmS, and Varkud satellite (VS) ribozymes, adenine in the hairpin, and VS and cytosine in the hepatitis delta virus (HDV) ribozyme. Crystal structures of the hairpin ribozyme (3) reveal the presence of guanine (G8) and adenine (A38) bases juxtaposed with the 2′-O and 5′-O, respectively, of the scissile phosphate, where they seem poised to act in general acid-base catalysis. This is consistent with the pH dependence of the reaction (4) and its variation with functional group modifications (5-8).In its simplest active form, the VS ribozyme comprises five helices (II through VI) organized by two three-way junctions, which acts in trans upon a substrate stem loop (helix I) with an internal loop that contains the scissile phosphate (Fig. 1). The loop also contains the critical G638 (9). A756 (10-13) is contained within an internal loop in helix VI. While no crystal structure of the VS ribozyme has yet been solved, a small-angle X-ray scattering-derived model plac...

show abstract

Section: Discussionmentioning

confidence: 99%

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

Wilson

Lü

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

120

View full text Add to dashboard Cite

show abstract

“…Like all the ribozymes except for those of the HDV group it uses a guanine N1 as general base in the cleavage reaction. But uniquely it appears to use a bound small molecule as the general acid (17,18,42,48,49). This creates an interesting precedent that immediately suggests how ribozymes might greatly expand their chemical repertoire by recruitment of coenzymes, either in an ancient RNA world, or even in contemporary biology (68).…”

Section: The Hammerhead Ribozyme -The Role Of a 2'-hydroxyl Groupmentioning

confidence: 99%

“…These cases are discussed below. Lastly, the GlmS ribozyme (10), which functions as a riboswitch, uses the amine of its glucosamine-6-phosphate as a general acid (17,18,42,48,49).…”

Section: The Role Of Nucleobases In Ribozyme Catalysismentioning

confidence: 99%

How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes

Lilley

2017

Biochemical Society Transactions

View full text Add to dashboard Cite

show abstract

“…Unlike traditional riboswitches, binding of GlcN6P does not induce a structural rearrangement within the RNA (Hampel and Tinsley 2006;Klein and Ferré-D'Amaré 2006;Cochrane et al 2007;Tinsley et al 2007). Instead, GlcN6P directly participates in the chemical reaction (McCarthy et al 2005;Klein and Ferré-D'Amaré 2006;Cochrane et al 2007). Within the crystal structures of the glmS ribozyme the primary amine of GlcN6P, the key functional group on the sugar, is within hydrogen bonding distance of the leaving group (Cochrane et al 2007;Klein et al 2007).…”

Section: Introductionmentioning

confidence: 99%

Riboswitch effectors as protein enzyme cofactors

Cochrane¹,

Strobel²

2008

RNA

View full text Add to dashboard Cite

The recently identified glmS ribozyme revealed that RNA enzymes, like protein enzymes, are capable of using small molecules as catalytic cofactors to promote chemical reactions. Flavin mononucleotide (FMN), S-adenosyl methionine (SAM), adenosyl cobalamin (AdoCbl), and thiamine pyrophosphate (TPP) are known ligands for RNA riboswitches in the control of gene expression, but are also catalytically powerful and ubiquitous cofactors in protein enzymes. If RNA, instead of just binding these molecules, could harness the chemical potential of the cofactor, it would significantly expand the enzymatic repertoire of ribozymes. Here we review the chemistry of AdoCbl, SAM, FMN, and TPP in protein enzymology and speculate on how these cofactors might have been used by ribozymes in the prebiotic RNA World or may still find application in modern biology.

show abstract

Ligand Requirements for glmS Ribozyme Self-Cleavage

Cited by 44 publications

References 0 publications

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme

How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes

Riboswitch effectors as protein enzyme cofactors

Contact Info

Product

Resources

About