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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
Article

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.

Key words

Berkeley Structural Genomics Center minimal organisms molecular function protein fold space structural genomics 

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Copyright information

© Springer 2005

Authors and Affiliations

  • Sung-Hou Kim
    • 1
    • 2
  • Dong Hae Shin
    • 2
  • Jinyu Liu
    • 2
  • Vaheh Oganesyan
    • 2
  • Shengfeng Chen
    • 1
  • Qian Steven Xu
    • 2
  • Jeong-Sun Kim
    • 1
  • Debanu Das
    • 2
  • Ursula Schulze-Gahmen
    • 2
  • Stephen R. Holbrook
    • 2
  • Elizabeth L. Holbrook
    • 2
  • Bruno A. Martinez
    • 2
  • Natalia Oganesyan
    • 2
  • Andy DeGiovanni
    • 2
  • Yun Lou
    • 2
  • Marlene Henriquez
    • 2
  • Candice Huang
    • 2
  • Jaru Jancarik
    • 1
  • Ramona Pufan
    • 2
  • In-Geol Choi
    • 1
  • John-Marc Chandonia
    • 2
  • Jingtong Hou
    • 2
  • Barbara Gold
    • 2
  • Hisao Yokota
    • 2
  • Steven E. Brenner
    • 2
  • Paul D. Adams
    • 2
  • Rosalind Kim
    • 2
  1. 1.Department of ChemistryUniversity of CaliforniaBerkeleyUSA
  2. 2.Berkeley Structural Genomics Center, Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyUSA

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