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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
S.-H. Kim D.H. Shin I.G. Choi U. Schulze-Gahmen S. Chen R. Kim (2003) J. Struct. Funct. Genomics 4 129–135 Occurrence Handle10.1023/A:1026200610644 Occurrence Handle14649297
M. Adams A. Joachimiak R. Kim G.T. Montelione J. Norvell (2004) J. Struct. Funct. Genomics 5 1–2 Occurrence Handle10.1023/B:JSFG.0000029244.65028.71 Occurrence Handle15263837
A. Bateman E. Birney R. Durbin S.R. Eddy K.L. Howe E.L. Sonnhammer (2000) Nucleic Acid Res. 28 263–266 Occurrence Handle10.1093/nar/28.1.263 Occurrence Handle10592242
S.F. Altschul W. Gish W. Miller E.W. Myers D.J. Lipman (1990) J. Mol. Biol. 215 403–410 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle2231712
J.C. Wootton (1994) Comput. Chem. 18 269–285 Occurrence Handle10.1016/0097-8485(94)85023-2 Occurrence Handle7952898
A. Lupas (1996) Methods Enzymol. 266 513–525 Occurrence Handle8743703
A. Krogh B. Larsson G. Heijne Particlevon E.L. Sonnhammer (2001) J. Mol. Biol. 305 567–580 Occurrence Handle10.1006/jmbi.2000.4315 Occurrence Handle11152613
B. Rost R. Casadio P. Fariselli C. Sander (1995) Protein Sci. 4 521–533 Occurrence Handle7795533
C. Aslanidis P.J. de Jong (1990) Nucleic Acids Res. 20 6069–6074
D. Busso R. Kim S.-H. Kim (2003) J. Biochem. Biophys. Methods 55 233–240 Occurrence Handle10.1016/S0165-022X(03)00049-6 Occurrence Handle12706907
N. Oganesyan S.-H. Kim R. Kim (2004) PharmaGenomics 7 22–26
J. Jancarik S.-H. Kim (1991) J. Appl. Crystallogr. 24 409–411 Occurrence Handle10.1107/S0021889891004430
J. Jancarik R. Pufan C. Hong S.-H. Kim R. Kim (2004) Acta Crystallogr. D 60 1670–1673 Occurrence Handle10.1107/S0907444904010972 Occurrence Handle15333951
S. Chen A.F. Yakunin E. Kuznetsova D. Busso R. Pufan M. Proudfoot R. Kim S.-H. Kim (2004) J. Biol. Chem. 279 31854–31862 Occurrence Handle10.1074/jbc.M401059200 Occurrence Handle15128743
L. Holm C. Sander (1995) Trends Biochem. Sci. 20 478–480 Occurrence Handle10.1016/S0968-0004(00)89105-7 Occurrence Handle8578593
J. Liu H. Yokota R. Kim S.-H. Kim (2004) Proteins 55 1082–1086 Occurrence Handle10.1002/prot.20119 Occurrence Handle15146506
V. Oganesyan R. Pufan A. DeGiovanni H. Yokota R. Kim S.-H. Kim (2004) Acta Crystallogr. D 60 1266–1271 Occurrence Handle10.1107/S0907444904009394 Occurrence Handle15213388
J. Hou G.E. Sims C. Zhang S.-H. Kim (2003) Proc. Natl. Acad. Sci. U.S.A. 100 2386–2390 Occurrence Handle10.1073/pnas.2628030100 Occurrence Handle12606708
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kim, SH., Shin, D.H., Liu, J. et al. Structural Genomics of Minimal Organisms and Protein Fold Space. J Struct Funct Genomics 6, 63–70 (2005). https://doi.org/10.1007/s10969-005-2651-9
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10969-005-2651-9