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Systematic classification of the His-Me finger superfamily.

ABSTRACT: The His-Me finger endonucleases, also known as HNH or ???-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins.

SUBMITTER: Jablonska J

PROVIDER: S-EPMC5714182 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Systematic classification of the His-Me finger superfamily.

Jablonska Jagoda J Matelska Dorota D Steczkiewicz Kamil K Ginalski Krzysztof K

Nucleic acids research 20171101 20

The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence simil ...[more]

PMID: 29040665

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Systematic classification of the His-Me finger superfamily.

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Systematic classification of the His-Me finger superfamily.

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