Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot

Kap Lim, Hong Zhang, Aleksandra Tempczyk, Wojciech Krajewski, Nicklas Bonander, John Toedt, Andrew Howard, Edward Eisenstein, Osnat Herzberg

Research output: Contribution to journalArticlepeer-review

87 Scopus citations


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 Å resolution, respectively. The molecule adopts an α/β 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.

Original languageEnglish (US)
Pages (from-to)56-67
Number of pages12
JournalProteins: Structure, Function and Genetics
Issue number1
StatePublished - Apr 1 2003

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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