1MXI

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

Summary for 1MXI

• Entry DOI: 10.2210/pdb1mxi/pdb
• Related: 1j85
• Descriptor: Hypothetical tRNA/rRNA methyltransferase HI0766, IODIDE ION, S-ADENOSYL-L-HOMOCYSTEINE, ... (4 entities in total)
• Functional Keywords: methyltransferase, s-adenosylhomocysteine, spou family, structure 2 function project, s2f, structural genomics, transferase
• Biological source: Haemophilus influenzae
• Cellular location: Cytoplasm (Potential): P44868
• Total number of polymer chains: 1
• Total formula weight: 18938.73

Authors

Lim, K.,Zhang, H.,Tempczyk, A.,Bonander, N.,Toedt, J.,Howard, A.,Eisenstein, E.,Herzberg, O.,Structure 2 Function Project (S2F) (deposition date: 2002-10-02, release date: 2003-02-25, Last modification date: 2024-02-14)

Primary citation

Lim, K.,Zhang, H.,Tempczyk, 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

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: 12596263
DOI: 10.1002/prot.10323

Experimental method

X-RAY DIFFRACTION (1.7 Å)