Structural genomics of minimal organisms and protein fold space

Sung Hou Kim, Dong Hae Shin, Jinyu Liu, Vaheh Oganesyan, Shengfeng Chen, Qian Steven Xu, Jeong Sun Kim, Debanu Das, Ursula Schulze-Gahmen, Stephen R. Holbrook, Elizabeth L. Holbrook, Bruno A. Martinez, Natalia Oganesyan, Andy DeGiovanni, Yun Lou, Marlene Henriquez, Candice Huang, Jaru Jancarik, Ramona Pufan, In-Geol Choi & 7 others John Marc Chandonia, Jingtong Hou, Barbara Gold, Hisao Yokota, Steven E. Brenner, Paul D. Adams, Rosalind Kim

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

The initial aim of the Berkeley Structural Genomics Center is to obtain a near-complete structural complement of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter fewer than 700 genes. To achieve this goal, the current protein targets have been selected starting with those predicted to be most tractable and likely to yield new structural and functional information. During the past 3 years, the semi-automated structural genomics pipeline has been set up from cloning, expression, purification, and ultimately to structural determination. The results from the pipeline substantially increased the coverage of the protein fold space of M. pneumoniae and M. genitalium. Furthermore, about 1/2 of the structures of 'unique' protein sequences revealed new and novel folds, and over 2/3 of the structures of previously annotated 'hypothetical proteins' inferred their molecular functions.

Original languageEnglish
Pages (from-to)63-70
Number of pages8
JournalJournal of Structural and Functional Genomics
Volume6
Issue number2-3
DOIs
Publication statusPublished - 2005 Sep 1
Externally publishedYes

Fingerprint

Genomics
Mycoplasma genitalium
Pneumonia
Proteins
Pipelines
Genes
Cloning
Pathogens
Purification
Organism Cloning

Keywords

  • Berkeley Structural Genomics Center
  • Minimal organisms
  • Molecular function
  • Protein fold space
  • Structural genomics

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Kim, S. H., Shin, D. H., Liu, J., Oganesyan, V., Chen, S., Xu, Q. S., ... Kim, R. (2005). Structural genomics of minimal organisms and protein fold space. Journal of Structural and Functional Genomics, 6(2-3), 63-70. https://doi.org/10.1007/s10969-005-2651-9

Structural genomics of minimal organisms and protein fold space. / Kim, Sung Hou; Shin, Dong Hae; Liu, Jinyu; Oganesyan, Vaheh; Chen, Shengfeng; Xu, Qian Steven; Kim, Jeong Sun; Das, Debanu; Schulze-Gahmen, Ursula; Holbrook, Stephen R.; Holbrook, Elizabeth L.; Martinez, Bruno A.; Oganesyan, Natalia; DeGiovanni, Andy; Lou, Yun; Henriquez, Marlene; Huang, Candice; Jancarik, Jaru; Pufan, Ramona; Choi, In-Geol; Chandonia, John Marc; Hou, Jingtong; Gold, Barbara; Yokota, Hisao; Brenner, Steven E.; Adams, Paul D.; Kim, Rosalind.

In: Journal of Structural and Functional Genomics, Vol. 6, No. 2-3, 01.09.2005, p. 63-70.

Research output: Contribution to journalArticle

Kim, SH, Shin, DH, Liu, J, Oganesyan, V, Chen, S, Xu, QS, Kim, JS, Das, D, Schulze-Gahmen, U, Holbrook, SR, Holbrook, EL, Martinez, BA, Oganesyan, N, DeGiovanni, A, Lou, Y, Henriquez, M, Huang, C, Jancarik, J, Pufan, R, Choi, I-G, Chandonia, JM, Hou, J, Gold, B, Yokota, H, Brenner, SE, Adams, PD & Kim, R 2005, 'Structural genomics of minimal organisms and protein fold space', Journal of Structural and Functional Genomics, vol. 6, no. 2-3, pp. 63-70. https://doi.org/10.1007/s10969-005-2651-9
Kim, Sung Hou ; Shin, Dong Hae ; Liu, Jinyu ; Oganesyan, Vaheh ; Chen, Shengfeng ; Xu, Qian Steven ; Kim, Jeong Sun ; Das, Debanu ; Schulze-Gahmen, Ursula ; Holbrook, Stephen R. ; Holbrook, Elizabeth L. ; Martinez, Bruno A. ; Oganesyan, Natalia ; DeGiovanni, Andy ; Lou, Yun ; Henriquez, Marlene ; Huang, Candice ; Jancarik, Jaru ; Pufan, Ramona ; Choi, In-Geol ; Chandonia, John Marc ; Hou, Jingtong ; Gold, Barbara ; Yokota, Hisao ; Brenner, Steven E. ; Adams, Paul D. ; Kim, Rosalind. / Structural genomics of minimal organisms and protein fold space. In: Journal of Structural and Functional Genomics. 2005 ; Vol. 6, No. 2-3. pp. 63-70.
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