title: Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
abstract: Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and the larger eukaryotic genomes are predicted to be completely sequenced within the next decade. In all genomes sequenced to date, a large portion of these organisms' predicted protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or cellular functions. Three-dimensional structures of these proteins may suggest biochemical or biophysical functions. Here we report the crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an ATP-mediated molecular switch, which we confirm by biochemical experiments. Furthermore, the structure reveals different ATP binding motifs that are shared among many homologous hypothetical proteins in this family. This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.
authors.affiliation: Physical Biosciences Division of Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
authors.forename: T I
authors.initials: TI
authors.lastname: Zarembinski
authors.forename: L W
authors.initials: LW
authors.lastname: Hung
authors.forename: H J
authors.initials: HJ
authors.lastname: Mueller-Dieckmann
authors.forename: K K
authors.initials: KK
authors.lastname: Kim
authors.forename: H
authors.initials: H
authors.lastname: Yokota
authors.forename: R
authors.initials: R
authors.lastname: Kim
authors.forename: S H
authors.initials: SH
authors.lastname: Kim
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D016678:Genome; D006860:Hydrogen Bonding; D017017:Methanococcus / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D016415:Sequence Alignment
chemical_list: C090796:ATP-binding protein, bacteria; D001426:Bacterial Proteins; D002352:Carrier Proteins; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases