The Novel Chemical Mechanism of the Twister Ribozyme

Timothy J. Wilson, Yijin Liu, Christof Domnick, Stephanie Kath-Schorr, David M J Lilley (Lead / Corresponding author)

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3′ to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5′ to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.

Original languageEnglish
Pages (from-to)6151-6162
Number of pages12
JournalJournal of the American Chemical Society
Volume138
Issue number19
Early online date6 May 2016
DOIs
Publication statusPublished - 18 May 2016

Fingerprint

Catalytic RNA
Phosphates
Catalysis
Substitution reactions
Acids
Adenine
Functional groups
Protons
Catalytic Domain
Nitrogen
Stabilization
Trajectories
Atoms

Cite this

Wilson, Timothy J. ; Liu, Yijin ; Domnick, Christof ; Kath-Schorr, Stephanie ; Lilley, David M J. / The Novel Chemical Mechanism of the Twister Ribozyme. In: Journal of the American Chemical Society. 2016 ; Vol. 138, No. 19. pp. 6151-6162.
@article{a5848e874b00450ca55df97be97a3eaa,
title = "The Novel Chemical Mechanism of the Twister Ribozyme",
abstract = "We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3′ to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5′ to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.",
author = "Wilson, {Timothy J.} and Yijin Liu and Christof Domnick and Stephanie Kath-Schorr and Lilley, {David M J}",
note = "We thank Dr. Darrin York and Colin Gaines (Rutgers) for discussion and data sharing, and Saira Ashraf for expert synthesis of RNA. The work was funded by Cancer Research UK (Program grant A11722 to DMJL) and Fonds der Chemischen Industrie (Liebig-fellowship LI 191/08 to SKS).",
year = "2016",
month = "5",
day = "18",
doi = "10.1021/jacs.5b11791",
language = "English",
volume = "138",
pages = "6151--6162",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "19",

}

The Novel Chemical Mechanism of the Twister Ribozyme. / Wilson, Timothy J.; Liu, Yijin; Domnick, Christof; Kath-Schorr, Stephanie; Lilley, David M J (Lead / Corresponding author).

In: Journal of the American Chemical Society, Vol. 138, No. 19, 18.05.2016, p. 6151-6162.

Research output: Contribution to journalArticle

TY - JOUR

T1 - The Novel Chemical Mechanism of the Twister Ribozyme

AU - Wilson, Timothy J.

AU - Liu, Yijin

AU - Domnick, Christof

AU - Kath-Schorr, Stephanie

AU - Lilley, David M J

N1 - We thank Dr. Darrin York and Colin Gaines (Rutgers) for discussion and data sharing, and Saira Ashraf for expert synthesis of RNA. The work was funded by Cancer Research UK (Program grant A11722 to DMJL) and Fonds der Chemischen Industrie (Liebig-fellowship LI 191/08 to SKS).

PY - 2016/5/18

Y1 - 2016/5/18

N2 - We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3′ to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5′ to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.

AB - We describe the multifactorial origins of catalysis by the twister ribozyme. We provide evidence that the adenine immediately 3′ to the scissile phosphate (A1) acts as a general acid. Substitution of ring nitrogen atoms indicates that very unusually the N3 of A1 is the proton donor to the oxyanion leaving group. A1 is accommodated in a specific binding pocket that raises its pKa toward neutrality, juxtaposes its N3 with the O5′ to be protonated, and helps create the in-line trajectory required for nucleophilic attack. A1 performs general acid catalysis while G33 acts as a general base. A 100-fold stereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stabilization of the transition state by the ribozyme, and functional group substitution at G33 indicates that its exocyclic N2 interacts directly with the scissile phosphate. A model of the ribozyme active site is proposed that accommodates these catalytic strategies.

UR - http://www.scopus.com/inward/record.url?scp=84971302103&partnerID=8YFLogxK

U2 - 10.1021/jacs.5b11791

DO - 10.1021/jacs.5b11791

M3 - Article

C2 - 27153229

AN - SCOPUS:84971302103

VL - 138

SP - 6151

EP - 6162

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 19

ER -