PMID: 11917146Mar 28, 2002Paper

In silico identification, structure prediction and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses

Protein Engineering
Janusz M Bujnicki, Leszek Rychlewski

Abstract

The Escherichia coli RrmJ gene product has recently been shown to be the 23S rRNA:U2552 specific 2'-O-ribose methyltransferase (MTase) (RrmJ). Its structure has been solved and refined to 1.5 A resolution, demonstrating conservation of the three-dimensional fold and key catalytic side chains with the vaccinia virus VP39 protein, which functions as an mRNA 5'm(7)G-cap-N-specific 2'-O-ribose MTase. Using the amino acid sequence of RrmJ as an initial probe in an iterative search of sequence databases, we identified a homologous domain in the sequence of the L protein of non-segmented, negative-sense, single-stranded RNA viruses. The plausibility of the prediction was confirmed by homology modeling and checking whether important residues at substrate/ligand-binding sites were conserved. The predicted structural compatibility and the conservation of the active site between the novel putative MTase domain and genuine 2'-O-ribose MTases, together with the available results of biochemical studies, strongly suggest that this domain is a 5'm(7)G-cap-N-specific 2'-O-ribose MTase (i.e. the cap 1 MTase). Evolutionary relationships between these proteins are also discussed.

References

Dec 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·S M Horikami, S A Moyer
Feb 21, 1994·FEBS Letters·D T JonesJ M Thornton
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Jan 1, 1993·Critical Reviews in Biochemistry and Molecular Biology·E V Koonin, V V Dolja
May 23, 1996·Nature·R W HooftE E Abola
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 15, 1997·Structure·G Varani
Oct 1, 1997·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·T F SmithR Lathrop
Jan 1, 1997·Methods in Enzymology·D EisenbergJ U Bowie
Jun 17, 1998·Nature Structural Biology·S Djordjevic, A M Stock
Mar 27, 1999·Journal of Molecular Evolution·L Aravind, E V Koonin
Mar 15, 2000·Protein Science : a Publication of the Protein Society·L RychlewskiA Godzik
May 9, 2000·Nature·K M ReinischS C Harrison
Jun 22, 2000·Journal of Molecular Biology·L A KelleyM J Sternberg
Sep 13, 2000·Molecular Cell·H BüglU Jakob
Oct 29, 2000·Advances in Virus Research·Y Furuichi, A J Shatkin
Aug 29, 2001·Bioinformatics·J M BujnickiL Rychlewski
Oct 18, 2001·Protein Science : a Publication of the Protein Society·J LundströmA Elofsson

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Citations

Feb 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Tomoaki OginoAmiya K Banerjee
Feb 20, 2010·Proceedings of the National Academy of Sciences of the United States of America·Eugene V Koonin, Bernard Moss
Apr 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Igor UlitskyBenny Chor
Dec 5, 2008·Journal of Virology·Andrea M Murphy, Valery Z Grdzelishvili
Apr 28, 2010·PLoS Pathogens·Mickaël BouvetEtienne Decroly
May 20, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jianrong LiSean P J Whelan
Sep 29, 2011·Virus Research·Tomoaki Ogino, Amiya K Banerjee
Apr 28, 2005·The Journal of Peptide Research : Official Journal of the American Peptide Society·P ChetalD Sahal
Jan 28, 2015·RNA Biology·Magdalena ByszewskaJanusz M Bujnicki
Jul 9, 2010·Virology·Andrea M MurphyValery Z Grdzelishvili
Jun 2, 2015·Frontiers in Microbiology·Robert Cox, Richard K Plemper
Mar 17, 2015·Virology·Eugene V KooninMart Krupovic
Feb 16, 2015·Virology·Jennifer L Hyde, Michael S Diamond
Jul 20, 2006·BMC Molecular Biology·Elzbieta PurtaJanusz M Bujnicki
Oct 18, 2005·BMC Structural Biology·Piotr Z Kozbial, Arcady R Mushegian
Mar 7, 2007·BMC Bioinformatics·Karolina L TkaczukJanusz M Bujnicki
Mar 6, 2007·Research in Veterinary Science·Pin Chun ShenLong Huw Lee
Jul 6, 2010·Journal of Molecular Biology·Mitsuo KurataniShigeyuki Yokoyama
Apr 12, 2016·Molecular BioSystems·Jillian N WhelanMichael N Teng
Nov 26, 2002·Journal of Molecular Recognition : JMR·Marc H V Van Regenmortel

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