The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.
NAR’s Breakthrough Articles present high-impact studies answering long-standing questions in the field of nucleic acids research and/or opening up new areas and mechanistic hypotheses for investigation. These articles are chosen by the Editors on the recommendation of Editorial Board Members and Referees. Articles are accompanied by a brief synopsis explaining the findings of the paper and where they fit in the broader context of nucleic acids research. They represent the very best papers published at NAR.
Non-homologous end joining is a means to repair DNA that is damaged due to double-stranded breaks. At an early stage during this DNA repair process, the protein 53BP1 is recruited to the site of damaged DNA. This study reveals a novel mechanism for regulation of 53BP1 recognition of damaged DNA that occurs through a newly identified post-translational modification of histone protein within chromatin. It contributes important details of a novel global cellular regulation system in repair of damaged DNA.
In all cells, rates of translation initiation vary widely, due to differences in mRNA sequence and structure. Multiple features of mRNA are thought to govern initiation and may explain why translation initiation rates cannot be accurately predicted. This study finds that the identities of four nucleotides upstream of the start codon tune translation in F. johnsoniae. Positive determinants include A-3, reminiscent of the Kozak sequence found in eukaryotic mRNAs. E. coli uses the same Kozak-like seq to tune initiation, indicating that this mechanism is used across diverse lineages. Removal of contacts between the conserved beta-hairpin of ribosomal protein uS7 and mRNA fails to diminish the contribution of A-3, suggesting an indirect means of recognition by the ribosome. mRNA secondary structure helps tune initiation in all organisms analyzed, and the trinucleotide AUG is underrepresented in the vicinity of the start codon, presumably to compensate for the lack of Shine-Delgarno sequence ...
