The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase.

The Journal of Biological Chemistry
Manisha YadavYuliang Wu

Abstract

The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation-seq, and cross-linking immunoprecipitation-seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our ...Continue Reading

References

Jun 11, 1996·Proceedings of the National Academy of Sciences of the United States of America·T Tomonaga, D Levens
Jan 1, 1996·Annual Review of Biochemistry·T M Lohman, K P Bjornson
Feb 13, 2001·Nucleic Acids Research·N V Grishin
Dec 31, 2002·Archives of Biochemistry and Biophysics·Antonella BandieraGiorgio Manzini
Sep 24, 2004·Biology of the Cell·Antje Ostareck-Lederer, Dirk H Ostareck
Feb 26, 2005·Nucleic Acids Research·M SidiqiM C J Wilce
Sep 30, 2005·The EMBO Journal·Barbara BeuthIan A Taylor
Mar 29, 2006·Proceedings of the National Academy of Sciences of the United States of America·Oleg DmitrievSvetlana Lutsenko
Oct 31, 2006·Nature Structural & Molecular Biology·Quansheng Yang, Eckhard Jankowsky
Dec 25, 2007·Journal of Molecular Biology·Vaishnavi Rajagopal, Smita S Patel
Apr 22, 2008·The FEBS Journal·Roberto ValverdeLynne Regan
Jun 25, 2008·Annual Review of Biophysics·Anna Marie Pyle
Aug 8, 2008·Nucleic Acids Research·María Flor García-MayoralAndres Ramos
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 19, 2008·Proceedings of the National Academy of Sciences of the United States of America·Lawrence R BenjaminDavid Levens
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Jul 1, 2009·Nature Methods·Audur MagnusdottirHelena Berglund
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 12, 2010·Current Opinion in Structural Biology·Margaret E Fairman-WilliamsEckhard Jankowsky
Jul 23, 2011·Nature Reviews. Molecular Cell Biology·Patrick Linder, Eckhard Jankowsky
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
May 2, 2012·Nucleic Acids Research·David HollingworthAndres Ramos
Nov 13, 2012·Nature Structural & Molecular Biology·Giuseppe NicastroAndres Ramos
Nov 24, 2012·Nucleic Acids Research·Ramanagouda Ramanagoudr-BhojappaKevin D Raney
Aug 22, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Mike P Williamson
Nov 30, 2013·International Journal of Molecular Sciences·Flora Sánchez-Jiménez, Víctor Sánchez-Margalet
Mar 19, 2014·Annual Review of Biochemistry·Inga Jarmoskaite, Rick Russell
Jan 28, 2015·Current Opinion in Structural Biology·Giuseppe NicastroAndres Ramos
May 8, 2015·Nature Protocols·Lawrence A KelleyMichael J E Sternberg
Jul 4, 2015·Nature Communications·Francesca FioriniVincent Croquette

❮ Previous
Next ❯

Software Mentioned

BEDTools
Phyre
Phyre 2
Quantity One
MACS2
SPARTA
Bowtie 2
MEME
NMRFx Processor
usegalaxy

Related Concepts

Related Feeds

ASBMB Publications

The American Society for Biochemistry and Molecular Biology (ASBMB) includes the Journal of Biological Chemistry, Molecular & Cellular Proteomics, and the Journal of Lipid Research. Discover the latest research from ASBMB here.