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PDB:3klr

Protein Name

Bovine H-protein

Species

Bos taurus (bovine)

Biological Context

Recently, the developments of X-ray crystallography enabled to determine many protein structures and pushed up the resolution limit and, the quality of protein structures. In high-resolution and well-refined structures, we can visualize multiple conformations of main and/or side chains and hydrogen atoms, accurate solvent structures, and determine anisotropic temperature factors. However, examples of high-resolution X-ray crystallography are still not numerous: only ~0.2% structures of the total are beyond 0.9 Å resolution. In this study, bovine H-protein was used as a model protein for high-resolution X-raycrystallography. The glycine cleavage system is a mitochondrial multi-enzyme system that consists of four different proteins (P-, H-, T- and L-proteins); together, these proteins catalyze the cleavage of glycine. This glycine cleavage system is widely distributed in animals, plants and bacteria. H-protein plays a central role in glycine cleavage. The lipoic acid covalently bound to a specific lysine residue of the H-protein interacts with specific sites on the P-, T- and L-proteins.

Structure Description

3klr3klr_x3klr_y

We determined the X-ray crystal structure of bovine H-protein at 0.88 Å resolution. Bovine H-protein mainly consists of two antiparallel β-sheets, and helices at the C-terminus joined to the main domain by a flexible linker. Multiple conformations were modeled for 29 residues and ~40% of hydrogen atoms were visualized.

In the measurement of high-resolution X-ray diffraction intensities, several experiments are needed to overcome the limitation of hardware. In this study, data collections for high-resolution diffraction data were carried out in three steps. The combination of these data sets made a difference in the visualization of hydrogen atoms, and the importance of low-resolution data was confirmed in the experimental data (Figure).

(figure) 2Fo-Fc (blue) and Fo-Fc (positive, green; negative, red) electron density maps. Green blobs show the hydrogen atoms.

Protein Data Bank (PDB)

References

Source

  • Higashiura, A. , Kurakane, T. , Matsuda, M. , Suzuki, M. , Inaka, K. , Sato, M. , Kobayashi, T. , Tanaka, T. , Tanaka, H. , Fujiwara, K. , Nakagawa, A.; "High-resolution X-ray crystal structure of bovine H-protein at 0.88 Angstrom resolution."; Acta Crystallogr.,Sect.D; (2010) 66:698-708.

Others

author: Akifumi Higashiura


Japanese version:PDB:3klr