1ONL
Crystal structure of Thermus thermophilus HB8 H-protein of the glycine cleavage system
Summary for 1ONL
| Entry DOI | 10.2210/pdb1onl/pdb |
| Descriptor | glycine cleavage system H protein (2 entities in total) |
| Functional Keywords | hybrid barrel-sandwich structure, structural genomics, riken structural genomics/proteomics initiative, rsgi, oxidoreductase |
| Biological source | Thermus thermophilus |
| Total number of polymer chains | 3 |
| Total formula weight | 42281.02 |
| Authors | Nakai, T.,Ishijima, J.,Masui, R.,Kuramitsu, S.,Kamiya, N.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-02-28, release date: 2003-08-26, Last modification date: 2023-10-25) |
| Primary citation | Nakai, T.,Ishijima, J.,Masui, R.,Kuramitsu, S.,Kamiya, N. Structure of Thermus thermophilus HB8 H-protein of the glycine-cleavage system, resolved by a six-dimensional molecular-replacement method. Acta Crystallogr.,Sect.D, 59:1610-1618, 2003 Cited by PubMed Abstract: The glycine-cleavage system is a multi-enzyme complex consisting of four different components (the P-, H-, T- and L-proteins). Recombinant H-protein corresponding to that from Thermus thermophilus HB8 has been overexpressed, purified and crystallized. Synchrotron radiation from BL44B2 at SPring-8 was used to collect a native data set to 2.5 A resolution. The crystals belonged to the hexagonal space group P6(5) and contained three molecules per asymmetric unit, with a solvent content of 39%. Because of the large number of molecules within a closely packed unit cell, this structure was solved by six-dimensional molecular replacement with the program EPMR using the pea H-protein structure as a search model and was refined to an R factor of 0.189 and a free R factor of 0.256. Comparison with the pea H-protein reveals two highly conserved regions surrounding the lipoyl-lysine arm. Both of these regions are negatively charged and each has additional properties that are conserved in H-proteins from many species, suggesting that these regions are involved in intermolecular interactions. One region has previously been proposed to constitute an interaction surface with T-protein, while the other may be involved in an interaction with P-protein. Meanwhile, the lipoyl-lysine arm of the T. thermophilus H-protein was found to be more flexible than that of the pea H-protein, supporting the hypothesis that H-protein does not form a stable complex with L-protein during the reaction. PubMed: 12925792DOI: 10.1107/S0907444903014975 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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