Crystal structure of A. aeolicus KsgA at 1.72-Angstrom resolution

Experimental Data Snapshot

  • Resolution: 1.68 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase.

Tu, C.Tropea, J.E.Austin, B.P.Court, D.L.Waugh, D.S.Ji, X.

(2009) Structure 17: 374-385

  • DOI: https://doi.org/10.1016/j.str.2009.01.010
  • Primary Citation of Related Structures:  
    3FTC, 3FTD, 3FTE, 3FTF

  • PubMed Abstract: 

    Among methyltransferases, KsgA and the reaction it catalyzes are conserved throughout evolution. However, the specifics of substrate recognition by the enzyme remain unknown. Here we report structures of Aquifex aeolicus KsgA, in its ligand-free form, in complex with RNA, and in complex with both RNA and S-adenosylhomocysteine (SAH, reaction product of cofactor S-adenosylmethionine), revealing critical structural information on KsgA-RNA and KsgA-SAH interactions. Moreover, the structures show how conformational changes that occur upon RNA binding create the cofactor-binding site. There are nine conserved functional motifs (motifs I-VIII and X) in KsgA. Prior to RNA binding, motifs I and VIII are flexible, each exhibiting two distinct conformations. Upon RNA binding, the two motifs become stabilized in one of these conformations, which is compatible with the binding of SAH. Motif X, which is also stabilized upon RNA binding, is directly involved in the binding of SAH.

  • Organizational Affiliation

    Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dimethyladenosine transferase249Aquifex aeolicus VF5Mutation(s): 0 
Gene Names: aq_1816ksgA
EC: 2.1.1
Find proteins for O67680 (Aquifex aeolicus (strain VF5))
Explore O67680 
Go to UniProtKB:  O67680
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67680
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.68 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.875α = 90
b = 53.577β = 90
c = 101.022γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2009-03-24 
  • Deposition Author(s): Tu, C., Ji, X.

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2023-09-06
    Changes: Refinement description