X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines.

Biochemistry
Yuan Lin, Clara L Kielkopf

Abstract

A pseudouridine-modified region of the U2 small nuclear (sn)RNA anneals with the intronic branchpoint sequence and positions a bulged adenosine to serve as the nucleophile in the first chemical step of pre-mRNA splicing. We have determined three X-ray structures of RNA oligonucleotides containing the pseudouridylated U2 snRNA and the branchpoint consensus sequences. The expected adenosine branchpoint is extrahelical in a 1.65 A resolution structure containing the mammalian consensus sequence variant and in a 2.10 A resolution structure containing a shortened Saccharomyces cerevisiae consensus sequence. The adenosine adjacent to the expected branchpoint is extrahelical in a third structure, which contains the intact yeast consensus sequence at 1.57 A resolution. The hydration and base stacking interactions mediated by the U2 snRNA pseudouridines correlate with the identity of the unpaired adenosine. The expected adenosine bulge is associated with a well-stacked pseudouridine, which is linked via an ordered water molecule to a neighboring nucleotide. In contrast, the bulge of the adjacent adenosine shifts the base stacking and disrupts the water-mediated interactions of the pseudouridine. These structural differences may contribu...Continue Reading

References

Mar 1, 1991·Acta Crystallographica. Section A, Foundations of Crystallography·T A JonesM Kjeldgaard
Aug 1, 1988·Journal of Biomolecular Structure & Dynamics·R Lavery, H Sklenar
Dec 1, 1984·Proceedings of the National Academy of Sciences of the United States of America·E B Keller, W A Noon
Jan 3, 1995·Proceedings of the National Academy of Sciences of the United States of America·M Egli, R V Gessner
Jul 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·T A Steitz, J A Steitz
Dec 25, 1995·Nucleic Acids Research·D R Davis
Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·A T BrüngerG L Warren
Jul 10, 1999·Genes & Development·E J SontheimerJ A Piccirilli
Feb 10, 2000·Acta Crystallographica. Section D, Biological Crystallography·Z DauterK R Rajashankar
Dec 2, 2000·Nature Structural Biology·R K SigelA M Pyle
Feb 23, 2002·Science·Lan Zhang, Jennifer A Doudna
Apr 3, 2002·Chemistry & Biology·Martin Egli
May 15, 2002·Cell·Tommaso VillaChristine Guthrie
Nov 12, 2002·Nature Structural Biology·Meredith I Newby, Nancy L Greenbaum
Jun 18, 2003·RNA·Saba Valadkhan, James L Manley
Jul 31, 2003·Molecular Cell·Melissa S Jurica, Melissa J Moore
Mar 16, 2004·Structure·Pascal AuffingerEric Westhof
May 18, 2004·RNA·Xinliang Zhao, Yi-Tao Yu
Jun 25, 2004·Nucleic Acids Research·Ian W DavisDavid C Richardson
Apr 21, 2005·RNA·Richard J Grainger, Jean D Beggs
May 27, 2005·Biochemical Society Transactions·S E Butcher, D A Brow
Oct 6, 2005·Genes & Development·Maria M Konarska, Charles C Query
Mar 3, 2006·Acta Crystallographica. Section D, Biological Crystallography·Felcy FabiolaMichael S Chapman
Mar 23, 2006·Journal of the American Chemical Society·Jörg C SchlattererNancy L Greenbaum

❮ Previous
Next ❯

Citations

Oct 7, 2011·Protein & Cell·Andrew T YuYi-Tao Yu
Nov 11, 2010·RNA·Matthew J SchellenbergAndrew M MacMillan
Aug 16, 2014·Nucleic Acids Research·Eric J MontemayorP John Hart
Feb 9, 2013·Trends in Biochemical Sciences·Junhui Ge, Yi-Tao Yu
Sep 8, 2009·Biochimica Et Biophysica Acta·Dustin B RitchieAndrew M MacMillan
Mar 13, 2016·Nucleic Acids Research·Jiazi TanXavier Roca
Oct 1, 2011·Wiley Interdisciplinary Reviews. RNA·Guowei WuYi-Tao Yu
Jan 27, 2015·RNA Biology·Felix SpenkuchMark Helm
Nov 13, 2008·Structure·Joseph SperlingRuth Sperling
Jun 17, 2018·Biological Chemistry·Markus T Bohnsack, Katherine E Sloan
Nov 21, 2019·Critical Reviews in Biochemistry and Molecular Biology·Clarisse van der Feltz, Aaron A Hoskins
Nov 26, 2019·Biochemical and Biophysical Research Communications·Eric Westhof
May 13, 2010·Biochemistry·Yuri Motorin, Mark Helm

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.