Abstract
Proteins are dynamic molecules that regulate a myriad of cellular functions; these functions may be regulated by protein post-translational modifications (PTMs) that mediate the activity, localization and interaction partners of proteins. Thus, understanding the meaning of a single PTM or the combination of several of them is essential to unravel the mechanisms of protein regulation. Yeast Amino Acid Modification (YAAM) (http://yaam.ifc.unam.mx) is a comprehensive database that contains information from 121 921 residues of proteins, which are post-translationally modified in the yeast model Saccharomyces cerevisiae. All the PTMs contained in YAAM have been confirmed experimentally. YAAM database maps PTM residues in a 3D canvas for 680 proteins with a known 3D structure. The structure can be visualized and manipulated using the most common web browsers without the need for any additional plugin. The aim of our database is to retrieve and organize data about the location of modified amino acids providing information in a concise but comprehensive and user-friendly way, enabling users to find relevant information on PTMs. Given that PTMs influence almost all aspects of the biology of both healthy and diseased cells, identifying and understanding PTMs is critical in the study of molecular and cell biology. YAAM allows users to perform multiple searches, up to three modifications at the same residue, giving the possibility to explore possible regulatory mechanism for some proteins. Using YAAM search engine, we found three different PTMs of lysine residues involved in protein translation. This suggests an important regulatory mechanism for protein translation that needs to be further studied. Database URL: http://yaam.ifc.unam.mx/
Highlights
Over time, living organisms have evolved through different regulation levels to control cell behaviour, not merely to survive and grow, and to trigger proper responses to external stimuli
Yeast Amino Acid Modification (YAAM) describes the exact residue of the protein active site, the important residues to bind ions (Calcium and other metals) of 3089 residues and 12 PostTranslational Modifications (PTMs) for a total of 121 921 residues (Supplementary Table S2)
A PTM can be included in the YAAM database only if the exact residue of such PTM was experimentally demonstrated by mass spectrometry (MS), point mutation or functional evidence
Summary
Over time, living organisms have evolved through different regulation levels to control cell behaviour, not merely to survive and grow, and to trigger proper responses to external stimuli One of these regulatory levels is the PostTranslational Modifications (PTMs), covalent modifications of a single or multiple amino acids in a protein. The main sources of information on PTMs come from mass spectrometry (MS) studies; these different MS methods used to obtain PTMs data, have different degrees of sensitivity and have generated results with various degrees of robustness [4,5,6] The emergence of these MS studies have led to an increase in the amount of data available in the literature, which in turn has created the need to collect and make this information easier to manage and analyse. This has allowed the development of new models and approaches for a better understanding of the mechanism of action of PTMs and, it has improved the interpretation of the relationships among these regulatory modifications [7]
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