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; John Marc Chandonia; Jingtong Hou; Barbara Gold; Hisao Yokota; Steven E. Brenner; Paul D. Adams; Rosalind Kim

doi:10.1007/s10969-005-2651-9

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 ChoiJohn Marc Chandonia, Jingtong Hou, Barbara Gold, Hisao Yokota, Steven E. Brenner, Paul D. Adams, Rosalind Kim

Research output: Contribution to journal › Article › peer-review

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 language	English
Pages (from-to)	63-70
Number of pages	8
Journal	Journal of Structural and Functional Genomics
Volume	6
Issue number	2-3
DOIs	https://doi.org/10.1007/s10969-005-2651-9
Publication status	Published - 2005 Sep
Externally published	Yes

Keywords

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

ASJC Scopus subject areas

Structural Biology
Biochemistry
Genetics

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10.1007/s10969-005-2651-9

Cite this

Kim, S. H., Shin, D. H., Liu, J., Oganesyan, V., Chen, S., Xu, Q. S., Kim, J. S., Das, D., Schulze-Gahmen, U., Holbrook, S. R., Holbrook, E. L., Martinez, B. A., Oganesyan, N., DeGiovanni, A., Lou, Y., Henriquez, M., Huang, C., Jancarik, J., Pufan, R., ... 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, 09.2005, p. 63-70.

Research output: Contribution to journal › Article › peer-review

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, IG, 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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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.",

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note = "Funding Information: We thank all the component members of BSGC for their efforts towards accomplishing the BSGC objectives. We gratefully acknowledge the support of NIH grant GM62412 for the structures cited in this article.",

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AU - Brenner, Steven E.

AU - Adams, Paul D.

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Structural genomics of minimal organisms and protein fold space

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Keywords

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