Journal of Structural and Functional Genomics

, Volume 15, Issue 3, pp 137–151 | Cite as

Structural insights of post-translational modification sites in the proteome of Thermus thermophilus

  • Ryoji Masui
  • Yoshio Takahata
  • Masao Inoue
  • Yota Iio
  • Hiroki Okanishi
  • Kwang Kim
  • Noriko Nakagawa
  • Kei Yura
  • Seiki Kuramitsu


Phosphorylation and acetylation are the most prevalent post-translational modifications (PTMs) detected in not only eukaryotes but also bacteria. We performed phosphoproteome and acetylome analyses of proteins from an extremely thermophilic eubacterium Thermus thermophilus HB8, and identified numerous phosphorylation and acetylation sites. To facilitate the elucidation of the structural aspects of these PTM events, we mapped the PTM sites on the known tertiary structures for the respective proteins and their homologs. Wu et al. (Mol Cell Proteomics 12:2701–2713, 2013) recently reported phosphoproteome analysis of proteins from T. thermophilus HB27. Therefore, we assessed the structural characteristics of these phosphorylation and acetylation sites on the tertiary structures of the identified proteins or their homologs. Our study revealed that many of the identified phosphosites are in close proximity to bound ligands, i.e., the numbers of ‘nearby’ and ‘peripheral’ phosphorylation sites represent 56 % (48/86 sites) of total identified phosphorylation sites. In addition, approximately 60 % of all phosphosites exhibited <10 % accessible surface area of their side chains, suggesting some structural rearrangement is required for phosphoryl transfer by kinases. Our findings also indicate that phosphorylation of a residue occurs more frequently at a flexible region of the protein, whereas lysine acetylation occurs more frequently in an ordered structure.


Phosphorylation Acetylation Posttranslational modification Crystal structure Ligand binding Accessible surface area 



Accessible surface area


Post-translational modification



This research was supported in part by Grant-in-Aid for Challenging Exploratory Research 25650008 (to RM). KY was supported by Platform for Drug Discovery, Informatics, and Structural Life Science from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Ryoji Masui
    • 1
  • Yoshio Takahata
    • 2
  • Masao Inoue
    • 1
  • Yota Iio
    • 1
  • Hiroki Okanishi
    • 1
  • Kwang Kim
    • 1
  • Noriko Nakagawa
    • 1
  • Kei Yura
    • 3
    • 4
    • 5
  • Seiki Kuramitsu
    • 1
    • 2
  1. 1.Department of Biological Sciences, Graduate School of ScienceOsaka UniversityOsakaJapan
  2. 2.Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
  3. 3.Graduate School of Humanities and SciencesOchanomizu UniversityTokyoJapan
  4. 4.Center for Informational BiologyOchanomizu UniversityTokyoJapan
  5. 5.National Institute of GeneticsShizuokaJapan

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