Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites

Daniel D. Seith, Jamie L. Bingaman, Andrew J. Veenis, Aileen C. Button, Philip C. Bevilacqua

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences among ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities among ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2′OH nucleophile (γ), neutralization of the nonbridging oxygens of the scissile phosphate (β), neutralization of the O5′ leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2′OH nucleophile by a guanine: one to acidify the 2′OH by hydrogen bond donation to it (γ′) and one to acidify the 2′OH by releasing it from nonproductive interactions by competitive hydrogen bonding (γ″). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies and help explain the absence of U at ribozyme active sites. The identified γ′ and γ″ catalytic strategies help unify the catalytic strategies shared among catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.

Original languageEnglish (US)
Pages (from-to)314-327
Number of pages14
JournalACS Catalysis
Volume8
Issue number1
DOIs
StatePublished - Jan 5 2018

Fingerprint

Catalytic RNA
Catalysis
Nucleophiles
Hydrogen bonds
Amidines
Deprotonation
Nucleic acids
Guanine
RNA
Viruses
Nucleic Acids
Functional groups
Conservation
Phosphates
Enzymes
Crystal structure
Chemical activation

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)

Cite this

Seith, Daniel D. ; Bingaman, Jamie L. ; Veenis, Andrew J. ; Button, Aileen C. ; Bevilacqua, Philip C. / Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites. In: ACS Catalysis. 2018 ; Vol. 8, No. 1. pp. 314-327.
@article{98d4ec0c6dd74c86a3dcda7452e2a675,
title = "Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites",
abstract = "A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences among ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities among ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2′OH nucleophile (γ), neutralization of the nonbridging oxygens of the scissile phosphate (β), neutralization of the O5′ leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2′OH nucleophile by a guanine: one to acidify the 2′OH by hydrogen bond donation to it (γ′) and one to acidify the 2′OH by releasing it from nonproductive interactions by competitive hydrogen bonding (γ″). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies and help explain the absence of U at ribozyme active sites. The identified γ′ and γ″ catalytic strategies help unify the catalytic strategies shared among catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.",
author = "Seith, {Daniel D.} and Bingaman, {Jamie L.} and Veenis, {Andrew J.} and Button, {Aileen C.} and Bevilacqua, {Philip C.}",
year = "2018",
month = "1",
day = "5",
doi = "10.1021/acscatal.7b02976",
language = "English (US)",
volume = "8",
pages = "314--327",
journal = "ACS Catalysis",
issn = "2155-5435",
publisher = "American Chemical Society",
number = "1",

}

Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites. / Seith, Daniel D.; Bingaman, Jamie L.; Veenis, Andrew J.; Button, Aileen C.; Bevilacqua, Philip C.

In: ACS Catalysis, Vol. 8, No. 1, 05.01.2018, p. 314-327.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes from Comparative Analysis of Active Sites

AU - Seith, Daniel D.

AU - Bingaman, Jamie L.

AU - Veenis, Andrew J.

AU - Button, Aileen C.

AU - Bevilacqua, Philip C.

PY - 2018/1/5

Y1 - 2018/1/5

N2 - A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences among ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities among ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2′OH nucleophile (γ), neutralization of the nonbridging oxygens of the scissile phosphate (β), neutralization of the O5′ leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2′OH nucleophile by a guanine: one to acidify the 2′OH by hydrogen bond donation to it (γ′) and one to acidify the 2′OH by releasing it from nonproductive interactions by competitive hydrogen bonding (γ″). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies and help explain the absence of U at ribozyme active sites. The identified γ′ and γ″ catalytic strategies help unify the catalytic strategies shared among catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.

AB - A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences among ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities among ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2′OH nucleophile (γ), neutralization of the nonbridging oxygens of the scissile phosphate (β), neutralization of the O5′ leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2′OH nucleophile by a guanine: one to acidify the 2′OH by hydrogen bond donation to it (γ′) and one to acidify the 2′OH by releasing it from nonproductive interactions by competitive hydrogen bonding (γ″). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies and help explain the absence of U at ribozyme active sites. The identified γ′ and γ″ catalytic strategies help unify the catalytic strategies shared among catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.

UR - http://www.scopus.com/inward/record.url?scp=85040308883&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040308883&partnerID=8YFLogxK

U2 - 10.1021/acscatal.7b02976

DO - 10.1021/acscatal.7b02976

M3 - Article

AN - SCOPUS:85040308883

VL - 8

SP - 314

EP - 327

JO - ACS Catalysis

JF - ACS Catalysis

SN - 2155-5435

IS - 1

ER -