1J85
Structure of YibK from Haemophilus influenzae (HI0766), a truncated sequence homolog of tRNA (guanosine-2'-O-) methyltransferase (SpoU)
Summary for 1J85
| Entry DOI | 10.2210/pdb1j85/pdb |
| Descriptor | YibK (2 entities in total) |
| Functional Keywords | methyltransferase, structural genomics, hypothetical protein, structure 2 function project, s2f, transferase |
| Biological source | Haemophilus influenzae Rd |
| Cellular location | Cytoplasm (Potential): P44868 |
| Total number of polymer chains | 1 |
| Total formula weight | 18427.41 |
| Authors | Lim, K.,Zhang, H.,Toedt, J.,Tempcyzk, A.,Krajewski, W.,Howard, A.,Eisenstein, E.,Herzberg, O.,Structure 2 Function Project (S2F) (deposition date: 2001-05-20, release date: 2003-02-25, Last modification date: 2024-02-07) |
| Primary citation | Lim, K.,Zhang, H.,Tempcyzk, A.,Krajewski, W.,Bonander, N.,Toedt, J.,Howard, A.,Eisenstein, E.,Herzberg, O. Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot Proteins, 51:56-67, 2003 Cited by PubMed Abstract: The crystal structures of YibK from Haemophilus influenzae (HI0766) have been determined with and without bound cofactor product S-adenosylhomocysteine (AdoHcy) at 1.7 and 2.0 A resolution, respectively. The molecule adopts an alpha/beta fold, with a topology that differs from that of the classical methyltransferases. Most notably, HI0766 contains a striking knot that forms the binding crevice for the cofactor. The knot formation is correlated with an alternative arrangement of the secondary structure units compared with the classical methyltransferases. Two loop regions undergo conformational changes upon AdoHcy binding. In contrast to the extended conformation of the cofactor seen in the classical methyltransferase structures, AdoHcy binds to HI0766 in a bent conformation. HI0766 and its close sequence relatives are all shorter versions of the more remotely related rRNA/tRNA methyltransferases of the spoU sequence family. We propose that the spoU sequence family contains the same core domain for cofactor binding as HI0766 but has an additional domain for substrate binding. The substrate-binding domain is absent in HI0766 sequence family and may be provided by another Haemophilus influenzae partner protein, which is yet to be identified. PubMed: 12596263DOI: 10.1002/prot.10323 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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