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Related Concept Videos

RNA Structure01:23

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.
Different Types of RNA Have the Same Basic Structure
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...
RNA Structure01:23

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.
Different Types of RNA Have the Same Basic Structure
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...
Transfer RNA Synthesis02:36

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 Structure01:19

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...
Transfer RNA Synthesis02:36

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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Structural basis for substrate selection by t7 RNA polymerase.

Dmitry Temiakov1, Vsevolod Patlan, Michael Anikin

  • 1Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA.

Cell
|March 16, 2004
PubMed
Summary

RNA polymerases (RNAPs) select substrates in an open conformation, unlike DNA polymerases. This discovery reveals a novel mechanism for substrate selection before catalytic activation, potentially universal across RNAPs.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Nucleotide polymerases are crucial for DNA replication and transcription fidelity.
  • Substrate selection in pol I DNA polymerases is linked to the transition from an open to a closed conformation.
  • The determinants of substrate selection in DNA polymerases are associated with the closed state.

Purpose of the Study:

  • To investigate if substrate selection mechanisms are conserved in single-subunit RNA polymerases (RNAPs).
  • To determine the structure of the T7 RNAP elongation complex with an incoming substrate analog.

Main Methods:

  • X-ray crystallography to determine the structure of the T7 RNAP elongation complex.
  • Structural analysis of substrate binding in the open conformation.
  • Modeling of multisubunit RNAPs.

Main Results:

  • T7 RNAP binds substrate in an open conformation, unlike DNA polymerases.
  • Substrate binding involves base pairing with the template base in the open state.
  • Tyrosine 639 (Tyr639) distinguishes between ribose and deoxyribose substrates.

Conclusions:

  • Substrate selection in RNAPs occurs prior to isomerization to the catalytically active conformation.
  • This mechanism represents a novel pathway for substrate selection in nucleotide polymerases.
  • The findings suggest this mechanism may be conserved across all RNAPs, including multisubunit forms.