Structure-based identification of a novel NTPase from Methanococcus jannaschii

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Almost half of the entire set of predicted genomic products from Methanococcus jannaschii are classified as functionally unknown hypothetical proteins. We present a structure-based identification of the biochemical function of a protein with an as yet unknown function from a M. jannaschii gene, Mj0226. The crystal structure of Mj0226 protein determined at 2.2 Å resolution reveals that the protein is a homodimer and each monomer folds into an elongated α/β structure of a new fold family. Comparisons of Mj0226 protein with protein structures in the database, however, indicate that one part of the protein is homologous to some of the nucleotide-binding proteins. Biochemical analysis shows that Mj0226 protein is a novel nucleotide triphosphatase that can efficiently hydrolyze nonstandard nucleotides such as XTP to XMP or ITP to IMP, but not the standard nucleotides, in the presence of Mg2+ or Mn2+ ions.

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Figure 1: a, A stereodiagram of the experimental (MIR) electron density map at 3.0 Å resolution.
Figure 2: A diagram showing the dimeric interface of Mj0226.
Figure 3: a, Structure comparison of Mj0226 protein (red) with the C-terminal domains of histidyl- (blue) and glycyl- (cyan) tRNA synthetases.
Figure 4: a, Thin layer chromatography showing the pyrophosphate releasing NTPase activities of Mj0226 with GTP.
Figure 5: Sequence alignment of Mj0226 with other homologous proteins.
Figure 6: a, A |Fo| - |Fc| map showing the AMPPNP.

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We are grateful to C.A. Caperelli (University of Cincinnati) for providing glycinamide ribonucleotide and 10-formyl-5,8-dideazafolate, and helpful comments on the GAR assay. We also thank B.K. Lee and J.S. Kim for the program SHEBA. This work was supported by funds from the Korea Institute of Science and Technology (KIST 2000 program), Korean Ministry of Science and Technology (Biotech 2000 program), Korean Ministry of Health and Welfare, Office of Biological and Environmental Research, Office of Energy Research, US Department of Energy, and Korean Academy of Science and Technology (a Young Scientist Award to Y.C.).

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Correspondence to Yunje Cho.

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