Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


An enzyme with a deep trefoil knot for the active-site architecture.

Nureki, O.Shirouzu, M.Hashimoto, K.Ishitani, R.Terada, T.Tamakoshi, M.Oshima, T.Chijimatsu, M.Takio, K.Vassylyev, D.G.Shibata, T.Inoue, Y.Kuramitsu, S.Yokoyama, S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1129-1137

  • DOI: https://doi.org/10.1107/s0907444902006601
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.

  • Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA 2'-O-RIBOSE METHYLTRANSFERASE274Thermus thermophilusMutation(s): 0 
EC: 2.1.1
Find proteins for Q7SID4 (Thermus thermophilus)
Explore Q7SID4 
Go to UniProtKB:  Q7SID4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SID4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.729α = 90
b = 66.729β = 90
c = 125.684γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references