3FTF

Crystal structure of A. aeolicus KsgA in complex with RNA and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.str.2009.01.010
  • Primary Citation of Related Structures:  3FTC, 3FTD, 3FTE

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dimethyladenosine transferase
A
249Aquifex aeolicus (strain VF5)Gene Names: rsmA (ksgA)
EC: 2.1.1.182
Find proteins for O67680 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67680
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*AP*AP*CP*CP*GP*UP*AP*GP*GP*GP*GP*AP*AP*CP*CP*UP*GP*CP*GP*GP*UP*U)-3'C,D22N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.130α = 90.00
b = 58.074β = 109.82
c = 68.981γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-01-12 
  • Released Date: 2009-03-24 
  • Deposition Author(s): Tu, C., Ji, X.

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance