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There are two types of acetylation processes widely occurred in proteins. The first Nα-terminal acetylation is catalyzed a variety of N-terminal acetyltransferases (NATs), which cotranslationally transfer acetyl moieties from acetyl-coenzyme A (Acetyl-CoA) to the α-amino (Nα) group of protein amino-terminal residues. Although Nα-terminal acetylation is rare in prokaryotes, it was estimated that about 85% of eukaryotic proteins are Nα-terminally modified (Polevoda et al., 2000; Polevoda et al., 2002). The second type is Nε-lysine acetylation, which specifically modifies ε-amino group of protein lysine residues (Yang et al., 2007; Shahbazian et al., 2007; Smith et al., 2009). Although Nε-lysine acetylation is less common, it's one of the most important and ubiquitous post-translational modifications conserved in prokaryotes and eukaryotes. Moreover, the acetylation and deacetylation are dynamically and temporally regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively (Yang et al., 2004; Lee et al., 2007).

  Beyond lysine acetylation, there are also a dozen of other types of post-translational modifications (PTMs) extensively occurred at lysine residues, such as ubiquitination (Gao, et al., 2013), methylation (Chen, et al., 2006), sumoylation (Ren, et al., 2009; Xue, et al., 2006), glycation (Priego-Capote, et al., 2010), butyrylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), crotonylation (Tan, et al., 2011), malonylation (Xie, et al., 2012), propionylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), succinylation (Xie, et al., 2012; Zhang, et al., 2011), neddylation (Rabut, et al., 2014; Soucy, et al., 2010), glutarylation (Tan, et al., 2014; Hirschey, et al., 2015), hydroxylation (Uzawa, et al., 2003), biotinylation (Hassan, et al., 2008; Kuroishi, et al., 2011), 2-hydroxyisobutyrylation (Dai, et al., 2014), lipoylation (Posner, et al., 2013), formylation (Jiang, et al., 2007), carboxylation (Jimenez-Morales, et al., 2014), phosphoglycerylation (Moellering, R. E. and B. F. Cravatt, 2013) and prokaryotic pupylation (Liu, et al., 2011). Thus, the lysine residue can be a "hotspot" of the PTM crosstalk (Lu, et al., 2011; Minguez, et al., 2012; van Noort, et al., 2012). Identification of these well-known or novel lysine modifications is fundamental for understanding their molecular mechanisms and regulatory roles.

  Recent advancement of proteomic techniques explosively expanded the number of PLM substrates and the discovery of novel PLMs. In view of the data accumulation, it has gradually emerged an urgent need for integrating of these sites together. Thus, we developed an integrative database of PLMD (Protein Lysine Modifications Database) for 20 types of protein lysine modifications, including 284780 modification events in 53501 proteins, which are divided into three categories consisted of 4 kinds of ubiquitin and ubiquitin-like modifications (Ub-UbLS), 9 kinds of acylation and 7 kinds of other PLMs, respectively. Because this database was adapted and extended from our CPLA (Compendium of Protein Lysine Acetylation) 1.0 database and CPLM (Compendium of Protein Lysine Modifications) 2.0 database, the current version of PLMD is 3.0. The database can be browse by either 1) types or 2) species.


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