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Comprehensive classification of the PIN domain-like superfamily

Matelska, D; Steczkiewicz, K; Ginalski, K; (2017) Comprehensive classification of the PIN domain-like superfamily. Nucleic Acids Research , 45 (12) pp. 6995-7020. 10.1093/nar/gkx494. Green open access

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Abstract

PIN-like domains constitute a widespread superfamily of nucleases, diverse in terms of the reaction mechanism, substrate specificity, biological function and taxonomic distribution. Proteins with PIN-like domains are involved in central cellular processes, such as DNA replication and repair, mRNA degradation, transcription regulation and ncRNA maturation. In this work, we identify and classify the most complete set of PIN-like domains to provide the first comprehensive analysis of sequence–structure–function relationships within the whole PIN domain-like superfamily. Transitive sequence searches using highly sensitive methods for remote homology detection led to the identification of several new families, including representatives of Pfam (DUF1308, DUF4935) and CDD (COG2454), and 23 other families not classified in the public domain databases. Further sequence clustering revealed relationships between individual sequence clusters and showed heterogeneity within some families, suggesting a possible functional divergence. With five structural groups, 70 defined clusters, over 100,000 proteins, and broad biological functions, the PIN domain-like superfamily constitutes one of the largest and most diverse nuclease superfamilies. Detailed analyses of sequences and structures, domain architectures, and genomic contexts allowed us to predict biological function of several new families, including new toxin-antitoxin components, proteins involved in tRNA/rRNA maturation and transcription/translation regulation.

Type: Article
Title: Comprehensive classification of the PIN domain-like superfamily
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/nar/gkx494
Publisher version: https://doi.org/10.1093/nar/gkx494
Language: English
Additional information: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Keywords: Science & Technology, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, TOXIN-ANTITOXIN SYSTEMS, PROTEIN-STRUCTURE PREDICTION, MESSENGER-RNA DECAY, DNA-POLYMERASE-I, RESTRICTION-MODIFICATION SYSTEMS, NUCLEOTIDE EXCISION-REPAIR, T5 FLAP ENDONUCLEASE, DIVALENT METAL-IONS, 18S RIBOSOMAL-RNA, CRYSTAL-STRUCTURE
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology
URI: https://discovery.ucl.ac.uk/id/eprint/10058978
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