CLASSIFICATION OF PROKARYOTIC DNA METHYLTRANSFERASES BY TOPOLOGY AND SEQUENCE SIMILARITY
ABSTRACT Prokaryotic DNA methyltrasferases (MTases) are essential enzymes within restriction- modification systems, preventing self DNA cleavage by restriction enzymes. They also participate in the regulation of gene expression, DNA repair, DNA replication and other processes.We propose a sequence-based homology classification of prokaryotic MTases, addressing a deficiency that has existed for over 20 years in the previous classification of MTases by Malone, Bujnicki into groups α, β, γ, etc.We defined 11 MTases classes on catalytic domain 3D topology by analysis available 3D structures and certain predicted 3D structures of MTases from AlfaFold DB. For each class we have selected from domain family’s databases HMM-profiles, that predicts in the hits the topology class on the base of sequence similarity with catalytic and SAM-binding subdomains. Based on the set of non-predicted MTases from DB REBASE we developed the algorithm for MTase topology classification and location conservative catalytic and SAM- binding motifs. The algorithm was applied to all available MTases. Topology classes are further subdivided into subclasses with the same domains architectures according Pfam DB.Homology classification allows to recover the MTases evolution as well as MTase annotations in existing and new sequences data sets.GRAPHICAL ABSTRACT <jats:fig id="ufig1" position="float" orientation="portrait" fig-type="figure"><jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="571470v3_ufig1" position="float" orientation="portrait" /></jats:fig>.
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Preprint| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
bioRxiv.org - (2024) vom: 04. Apr. Zur Gesamtaufnahme - year:2024 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Samokhina, Maria [VerfasserIn] |
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| Links: |
Volltext [kostenfrei] |
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| doi: |
10.1101/2023.12.13.571470 |
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| PPN (Katalog-ID): |
XBI04187711X |
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| 520 | |a ABSTRACT Prokaryotic DNA methyltrasferases (MTases) are essential enzymes within restriction- modification systems, preventing self DNA cleavage by restriction enzymes. They also participate in the regulation of gene expression, DNA repair, DNA replication and other processes.We propose a sequence-based homology classification of prokaryotic MTases, addressing a deficiency that has existed for over 20 years in the previous classification of MTases by Malone, Bujnicki into groups α, β, γ, etc.We defined 11 MTases classes on catalytic domain 3D topology by analysis available 3D structures and certain predicted 3D structures of MTases from AlfaFold DB. For each class we have selected from domain family’s databases HMM-profiles, that predicts in the hits the topology class on the base of sequence similarity with catalytic and SAM-binding subdomains. Based on the set of non-predicted MTases from DB REBASE we developed the algorithm for MTase topology classification and location conservative catalytic and SAM- binding motifs. The algorithm was applied to all available MTases. Topology classes are further subdivided into subclasses with the same domains architectures according Pfam DB.Homology classification allows to recover the MTases evolution as well as MTase annotations in existing and new sequences data sets.GRAPHICAL ABSTRACT <jats:fig id="ufig1" position="float" orientation="portrait" fig-type="figure"><jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="571470v3_ufig1" position="float" orientation="portrait" /></jats:fig> | ||
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