Structure of YibK from Haemophilus influenzae (HI0766), a truncated sequence homolog of tRNA (guanosine-2'-O-) methyltransferase (SpoU)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 

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

Lim, K.Zhang, H.Tempcyzk, A.Krajewski, W.Bonander, N.Toedt, J.Howard, A.Eisenstein, E.Herzberg, O.

(2003) Proteins 51: 56-67

  • DOI: https://doi.org/10.1002/prot.10323
  • Primary Citation of Related Structures:  
    1J85, 1MXI

  • 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.

  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YibK160Haemophilus influenzae Rd KW20Mutation(s): 0 
Gene Names: HI0766
EC: 2.1.1
Find proteins for P44868 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44868 
Go to UniProtKB:  P44868
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44868
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.195 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.37α = 90
b = 40.37β = 90
c = 165.82γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references