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 | |
| Publication status | Published - 2005 Sep 1 |
| Externally published | Yes |
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Keywords
- Berkeley Structural Genomics Center
- Minimal organisms
- Molecular function
- Protein fold space
- Structural genomics
ASJC Scopus subject areas
- Genetics
- Structural Biology
- Biochemistry
Cite this
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 journal › Article
}
TY - JOUR
T1 - Structural genomics of minimal organisms and protein fold space
AU - Kim, Sung Hou
AU - Shin, Dong Hae
AU - Liu, Jinyu
AU - Oganesyan, Vaheh
AU - Chen, Shengfeng
AU - Xu, Qian Steven
AU - Kim, Jeong Sun
AU - Das, Debanu
AU - Schulze-Gahmen, Ursula
AU - Holbrook, Stephen R.
AU - Holbrook, Elizabeth L.
AU - Martinez, Bruno A.
AU - Oganesyan, Natalia
AU - DeGiovanni, Andy
AU - Lou, Yun
AU - Henriquez, Marlene
AU - Huang, Candice
AU - Jancarik, Jaru
AU - Pufan, Ramona
AU - Choi, In-Geol
AU - Chandonia, John Marc
AU - Hou, Jingtong
AU - Gold, Barbara
AU - Yokota, Hisao
AU - Brenner, Steven E.
AU - Adams, Paul D.
AU - Kim, Rosalind
PY - 2005/9/1
Y1 - 2005/9/1
N2 - 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.
AB - 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.
KW - Berkeley Structural Genomics Center
KW - Minimal organisms
KW - Molecular function
KW - Protein fold space
KW - Structural genomics
UR - http://www.scopus.com/inward/record.url?scp=26444567767&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=26444567767&partnerID=8YFLogxK
U2 - 10.1007/s10969-005-2651-9
DO - 10.1007/s10969-005-2651-9
M3 - Article
C2 - 16211501
AN - SCOPUS:26444567767
VL - 6
SP - 63
EP - 70
JO - Journal of Structural and Functional Genomics
JF - Journal of Structural and Functional Genomics
SN - 1345-711X
IS - 2-3
ER -