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tRNA Activation

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...

tRNA Activation

tRNA Activation

Transfer RNA Synthesis

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

ATP and Macromolecule Synthesis

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Biological macromolecules are organic compounds, predominantly composed of carbon atoms. The carbon atoms are covalently bonded with hydrogen, oxygen, nitrogen, and other minor elements. There are four major biological macromolecule classes: carbohydrates, lipids, proteins, and nucleic acids.
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DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Structural basis for TNA synthesis by an engineered TNA polymerase.

Nicholas Chim¹, Changhua Shi¹, Sujay P Sau¹

¹Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine, CA, 92697-3958, USA.

Nature Communications

|November 29, 2017

Summary

Researchers engineered a polymerase for xeno-nucleic acid (XNA) synthesis. Structural analysis revealed a suboptimal active site geometry limiting TNA synthesis efficiency, guiding future polymerase engineering.

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Area of Science:

Biochemistry
Molecular Biology
Synthetic Biology

Background:

Darwinian evolution experiments with xeno-nucleic acids (XNA) require efficient polymerases for DNA-XNA information transfer.
Current XNA polymerases exhibit lower activity compared to natural DNA polymerases.

Purpose of the Study:

To elucidate the structural basis for template-dependent selection and extension of alpha-(L)-threofuranosyl nucleic acid (TNA) triphosphates by the engineered polymerase Kod-RI.
To identify structural limitations hindering TNA synthesis efficiency.

Main Methods:

X-ray crystallography was used to determine five distinct structures: apo, binary, open ternary, closed ternary, and translocated product states.
Comparative structural analysis of these states to understand conformational changes and interactions during TNA synthesis.

Main Results:

The study details the interactions and conformational shifts enabling TNA triphosphate selection and extension by Kod-RI.
Structural analysis revealed a sub-optimal binding geometry in the active site of the closed ternary complex.
This sub-optimal geometry directly explains the observed slow catalytic rate of TNA synthesis.

Conclusions:

The determined structures provide a detailed mechanistic understanding of TNA synthesis by Kod-RI.
The identified active site limitations offer a crucial framework for engineering improved TNA polymerase variants with enhanced activity.