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Literature DB >> 15574497

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.

Nizar N Batada¹, Kenneth D Westover, David A Bushnell, Michael Levitt, Roger D Kornberg.

Abstract

Nucleoside triphosphates (NTPs) diffuse to the active center of RNA polymerase II through a funnel-shaped opening that narrows to a negatively charged pore. Computer simulation shows that the funnel and pore reduce the rate of diffusion by a factor of approximately 2 x 10(-7). The resulting limitation on the rate of RNA synthesis under conditions of low NTP concentration may be overcome by NTP binding to an entry site adjacent to the active center. Binding to the entry site greatly enhances the lifetime of an NTP in the active center region, and it prevents "backtracking" and the consequent occlusion of the active site.

Entities: Chemical

Mesh：

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Year: 2004 PMID： 15574497 PMCID： PMC536049 DOI： 10.1073/pnas.0408168101

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

15 in total

Review 10. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site.

Authors: Sangwook Wu; William A Beard; Lee G Pedersen; Samuel H Wilson
Journal: Chem Rev Date: 2013-12-20 Impact factor: 60.622

Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center.

1. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.

2. Architecture of RNA polymerase II and implications for the transcription mechanism.

3. Electrostatics of nanosystems: application to microtubules and the ribosome.

4. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

5. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.

6. Structural basis for substrate selection by t7 RNA polymerase.

7. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.

8. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase.

9. Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography.

10. The structural mechanism of translocation and helicase activity in T7 RNA polymerase.

1. pH-dependent conformational switch activates the inhibitor of transcription elongation.

2. Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro.

3. Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.

Review 4. Evolution of multisubunit RNA polymerases in the three domains of life.

5. RNA polymerase II conserved protein domains as platforms for protein-protein interactions.

6. Millisecond dynamics of RNA polymerase II translocation at atomic resolution.

Review 7. The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.

Review 8. Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.

9. Templated nucleoside triphosphate binding to a noncatalytic site on RNA polymerase regulates transcription.

Review 10. Structural comparison of DNA polymerase architecture suggests a nucleotide gateway to the polymerase active site.