PLMD: An updated data resource of protein lysine modifications

Haodong Xu; Jiaqi Zhou; Shaofeng Lin; Wankun Deng; Ying Zhang; Yu Xue

doi:10.1016/j.jgg.2017.03.007

Volume 44 Issue 5

May 2017

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Article Navigation > Journal of Genetics and Genomics > 2017 > 44(5): 243-250

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PLMD: An updated data resource of protein lysine modifications

doi: 10.1016/j.jgg.2017.03.007

Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan 430074, China

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Corresponding author: E-mail address: xueyu@hust.edu.cn (Yu Xue)
Received Date: 2016-12-12
Revised Date: 2017-01-26
Accepted Date: 2017-03-30

Available Online: 2017-05-03

Publish Date: 2017-05-20

Abstract

Abstract

Post-translational modifications (PTMs) occurring at protein lysine residues, or protein lysine modifications (PLMs), play critical roles in regulating biological processes. Due to the explosive expansion of the amount of PLM substrates and the discovery of novel PLM types, here we greatly updated our previous studies, and presented a much more integrative resource of protein lysine modification database (PLMD). In PLMD, we totally collected and integrated 284,780 modification events in 53,501 proteins across 176 eukaryotes and prokaryotes for up to 20 types of PLMs, including ubiquitination, acetylation, sumoylation, methylation, succinylation, malonylation, glutarylation, glycation, formylation, hydroxylation, butyrylation, propionylation, crotonylation, pupylation, neddylation, 2-hydroxyisobutyrylation, phosphoglycerylation, carboxylation, lipoylation and biotinylation. Using the data set, a motif-based analysis was performed for each PLM type, and the results demonstrated that different PLM types preferentially recognize distinct sequence motifs for the modifications. Moreover, various PLMs synergistically orchestrate specific cellular biological processes by mutual crosstalks with each other, and we totally found 65,297 PLM events involved in 90 types of PLM co-occurrences on the same lysine residues. Finally, various options were provided for accessing the data, while original references and other annotations were also present for each PLM substrate. Taken together, we anticipated the PLMD database can serve as a useful resource for further researches of PLMs. PLMD 3.0 was implemented in PHP + MySQL and freely available at http://plmd.biocuckoo.org.
- Post-translational modification (PTM),
- Protein lysine modification (PLM),
- Ubiquitination,
- Acetylation,
- PTM crosstalk

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