The structure of a nucleolytic ribozyme that employs a catalytic metal ion

Yijin Liu, Timothy Wilson, David Lilley (Lead / Corresponding author)

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Abstract

The TS ribozyme (originally called twister-sister) is a nucleolytic catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasi-helical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an innersphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.
Original languageEnglish
Pages (from-to)508-513
Number of pages7
JournalNature Chemical Biology
Volume13
Issue number5
Early online date6 Mar 2017
DOIs
Publication statusPublished - May 2017

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Catalytic RNA
Metals
Ions
Phosphates
RNA
Hydrogen Bonding
Protons
Ligands
Water

Keywords

  • RNA catalysis
  • metal ions
  • RNA structure
  • X-ray crysallography

Cite this

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title = "The structure of a nucleolytic ribozyme that employs a catalytic metal ion",
abstract = "The TS ribozyme (originally called twister-sister) is a nucleolytic catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasi-helical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an innersphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.",
keywords = "RNA catalysis, metal ions, RNA structure, X-ray crysallography",
author = "Yijin Liu and Timothy Wilson and David Lilley",
note = "Funding: CRUK for program support A18604 (to DMJL), the Wellcome Trust for the in-house diffractometer and ESRF for synchrotron beam time.",
year = "2017",
month = "5",
doi = "10.1038/nchembio.2333",
language = "English",
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pages = "508--513",
journal = "Nature Chemical Biology",
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TY - JOUR

T1 - The structure of a nucleolytic ribozyme that employs a catalytic metal ion

AU - Liu, Yijin

AU - Wilson, Timothy

AU - Lilley, David

N1 - Funding: CRUK for program support A18604 (to DMJL), the Wellcome Trust for the in-house diffractometer and ESRF for synchrotron beam time.

PY - 2017/5

Y1 - 2017/5

N2 - The TS ribozyme (originally called twister-sister) is a nucleolytic catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasi-helical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an innersphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.

AB - The TS ribozyme (originally called twister-sister) is a nucleolytic catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasi-helical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an innersphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.

KW - RNA catalysis

KW - metal ions

KW - RNA structure

KW - X-ray crysallography

U2 - 10.1038/nchembio.2333

DO - 10.1038/nchembio.2333

M3 - Article

C2 - 28263963

VL - 13

SP - 508

EP - 513

JO - Nature Chemical Biology

JF - Nature Chemical Biology

SN - 1552-4450

IS - 5

ER -