Skip Navigation

Nucleic Acids Research 2005 33(16):5226-5234; doi:10.1093/nar/gki841
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (9711K) Freely available
Right arrow Screen PDF (1044K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (2)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Oparina, N. J.
Right arrow Articles by Kisselev, L. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Oparina, N. J.
Right arrow Articles by Kisselev, L. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 14 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications

Nina J. Oparina*, Olga V. Kalinina1, Mikhail S. Gelfand2,3 and Lev L. Kisselev

Engelhardt Institute of Molecular Biology Russian Academy of Sciences Vavilov street 32, Moscow 119991, Russia 1Department of Bioengineering and Bioinformatics, Moscow State University Vorob'evy Gory, 1-73, Moscow 119992, Russia 2Institute for Information Transmission Problems, Russian Academy of Sciences Bolshoi Karetnyi per., 19, Moscow 127994, Russia 3State Scientific Centre GosNIIGenetika 1st Dorozhny pr. 1, Moscow, 113545, Russia

*To whom correspondence should be addressed. Tel: +7 095 1351419; Fax: +7 095 1351405; Email: nixie{at}eimb.ru

Received June 20, 2005. Revised August 30, 2005. Accepted August 30, 2005.

Termination of protein synthesis is promoted in ribosomes by proper stop codon discrimination by class 1 polypeptide release factors (RFs). A large set of prokaryotic RFs differing in stop codon specificity, RF1 for UAG and UAA, and RF2 for UGA and UAA, was analyzed by means of a recently developed computational method allowing identification of the specificity-determining positions (SDPs) in families composed of proteins with similar but not identical function. Fifteen SDPs were identified within the RF1/2 superdomain II/IV known to be implicated in stop codon decoding. Three of these SDPs had particularly high scores. Five residues invariant for RF1 and RF2 [invariant amino acid residues (IRs)] were spatially clustered with the highest-scoring SDPs that in turn were located in two zones within the SDP/IR area. Zone 1 (domain II) included PxT and SPF motifs identified earlier by others as ‘discriminator tripeptides’. We suggest that IRs in this zone take part in the recognition of U, the first base of all stop codons. Zone 2 (domain IV) possessed two SDPs with the highest scores not identified earlier. Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.