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novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

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Schematic representation of five unusual PTMs of proteins. For each PTM chemical structures of the amino acid and modified amino acid have been depicted.
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bav039-F1: Schematic representation of five unusual PTMs of proteins. For each PTM chemical structures of the amino acid and modified amino acid have been depicted.

Mentions: Post-translational modifications (PTMs) of proteins are a crucial strategy used by both prokaryotes and eukaryotes to modulate and regulate cellular processes. Modification of proteins can range from the addition of a small chemical moiety such as phosphate to the addition of peptides like ubiquitin and SUMO or the covalent cleavage of peptide backbone (1). The modifications play a central role in intracellular signaling; signaling pathways associated with host-pathogen interactions (2) as well as the biosynthesis of many bioactive natural products like lantibiotics (3) and so enables proteins to acquire new functions. Therefore, the identification of enzymes involved in novel PTMs by genome mining has become an area of major interest. The exponential increase in genome sequences and the experimental characterization of a large number of amino acid modifications in proteins has created a bottleneck in connecting known PTMs to the genes catalyzing them (4). Therefore, it is necessary to decipher the various biochemical pathways associated with PTM catalyzing enzymes by in silico genome analysis. PTMs like phosphorylation, glycosylation, SUMOylation have been characterized extensively and a number of bioinformatics tools are available for analysis of the enzymes involved in their catalysis. O-GLYCBASE (5) and Phosphso.ELM (6) are some examples of databases associated with specific classes of PTMs. In contrast to these well-known PTMs, no user friendly tools are available for the identification and analysis of enzymes associated with newly discovered novel PTMs (Figure 1) like AMPylation (7) and Eliminylation (8) and unusual PTMs like Sulfation (9), Hydroxylation (10) and Deamidation (11). Even though these PTMs occur less frequently, they play a crucial role in structural and functional diversification of the proteome and their role in expanding the metabolic and signaling capacities of an organism cannot be underestimated (12).Figure 1.


novPTMenzy: a database for enzymes involved in novel post-translational modifications.

Khater S, Mohanty D - Database (Oxford) (2015)

Schematic representation of five unusual PTMs of proteins. For each PTM chemical structures of the amino acid and modified amino acid have been depicted.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414956&req=5

bav039-F1: Schematic representation of five unusual PTMs of proteins. For each PTM chemical structures of the amino acid and modified amino acid have been depicted.
Mentions: Post-translational modifications (PTMs) of proteins are a crucial strategy used by both prokaryotes and eukaryotes to modulate and regulate cellular processes. Modification of proteins can range from the addition of a small chemical moiety such as phosphate to the addition of peptides like ubiquitin and SUMO or the covalent cleavage of peptide backbone (1). The modifications play a central role in intracellular signaling; signaling pathways associated with host-pathogen interactions (2) as well as the biosynthesis of many bioactive natural products like lantibiotics (3) and so enables proteins to acquire new functions. Therefore, the identification of enzymes involved in novel PTMs by genome mining has become an area of major interest. The exponential increase in genome sequences and the experimental characterization of a large number of amino acid modifications in proteins has created a bottleneck in connecting known PTMs to the genes catalyzing them (4). Therefore, it is necessary to decipher the various biochemical pathways associated with PTM catalyzing enzymes by in silico genome analysis. PTMs like phosphorylation, glycosylation, SUMOylation have been characterized extensively and a number of bioinformatics tools are available for analysis of the enzymes involved in their catalysis. O-GLYCBASE (5) and Phosphso.ELM (6) are some examples of databases associated with specific classes of PTMs. In contrast to these well-known PTMs, no user friendly tools are available for the identification and analysis of enzymes associated with newly discovered novel PTMs (Figure 1) like AMPylation (7) and Eliminylation (8) and unusual PTMs like Sulfation (9), Hydroxylation (10) and Deamidation (11). Even though these PTMs occur less frequently, they play a crucial role in structural and functional diversification of the proteome and their role in expanding the metabolic and signaling capacities of an organism cannot be underestimated (12).Figure 1.

Bottom Line: Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation.It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation.The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.

Show MeSH