ArticleNucleic acids research2017
Comprehensive classification of the PIN domain-like superfamily.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
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- Specialized RNA decay fine-tunes monogenic antigen expression in Trypanosoma brucei.Nature microbiology · 2026Article
- Composite SMG5-SMG6 PIN domain formation is essential for NMD.Nature communications · 2026Article
- Diversity and distribution of bacterial DNA polymerases.Nucleic acids research · 2026Article
- KHNYN is a manganese-dependent endoribonuclease required for ZAP-mediated antiviral restriction.Nucleic acids research · 2025Article
- Structural insights into higher-order natural RNA-only multimers.Nature structural & molecular biology · 2025Article
- Remodeling of RNA-binding proteome and RNA-mediated regulation as a new layer of control of sporulation.mSystems · 2025Article
- Bacterial/archaeal protein-only RNase P: complementation inRNA (New York, N.Y.) · 2025Article
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- Identification of novel genes responsible for a pollen killer present in local natural populations of Arabidopsis thaliana.PLoS genetics · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- MUT-7 exoribonuclease activity and localization are mediated by an ancient domain.Nucleic acids research · 2024Article
- RNA processing by the CRISPR-associated NYN ribonuclease.The Biochemical journal · 2024Article
- Clocking out and letting go to unleash green biotech applications in a photosynthetic host.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms.Cell death discovery · 2024Review
- Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes.The Journal of biological chemistry · 2024Review
- Investigation of protein family relationships with deep learning.Bioinformatics advances · 2024Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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