3OFK

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of NodS N-Methyltransferase from Bradyrhizobium japonicum in Ligand-Free Form and as SAH Complex.

Cakici, O.Sikorski, M.Stepkowski, T.Bujacz, G.Jaskolski, M.

(2010) J.Mol.Biol. 404: 874-889

  • DOI: 10.1016/j.jmb.2010.10.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NodS is an S-adenosyl-L-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule th ...

    NodS is an S-adenosyl-L-methionine (SAM)-dependent N-methyltransferase that is involved in the biosynthesis of Nod factor (NF) in rhizobia, which are bacterial symbionts of legume plants. NF is a modified chitooligosaccharide (COS) signal molecule that is recognized by the legume host, where it initiates symbiotic processes leading to atmospheric nitrogen fixation. We report the crystal structure of recombinant NodS protein from Bradyrhizobium japonicum, which infects lupine and serradella legumes. Two crystal forms--ligand-free NodS and NodS in complex with S-adenosyl-L-homocysteine, which is a by-product of the methylation reaction--were obtained, and their structures were refined to resolutions of 2.43 Å and 1.85 Å, respectively. Although the overall fold (consisting of a seven-stranded β-sheet flanked by layers of helices) is similar to those of other SAM-dependent methyltransferases, NodS has specific features reflecting the unique character of its oligosaccharide substrate. In particular, the N-terminal helix and its connecting loop get ordered upon SAM binding, thereby closing the methyl donor cavity and shaping a long surface canyon that is clearly the binding site for the acceptor molecule. Comparison of the two structural forms of NodS suggests that there are also other conformational changes taking place upon the binding of the donor substrate. As an enzyme that methylates a COS substrate, NodS is the first example among all SAM-dependent methyltransferases to have its three-dimensional structure elucidated. Gaining insight about how NodS binds its donor and acceptor substrates helps to better understand the mechanism of NodS activity and the basis of its functional difference in various rhizobia.


    Related Citations: 
    • Cloning, expression, purification, crystallization and preliminary X-ray analysis of NodS N-methyltransferase from Bradyrhizobium japonicum WM9
      Cakici, O.,Sikorski, M.,Stepkowski, T.,Bujacz, G.,Jaskolski, M.
      (2008) Acta Crystallogr.,Sect.F F64: 1149


    Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nodulation protein S
A, B, C, D
216Bradyrhizobium sp. (strain WM9)Mutation(s): 0 
Gene Names: nodS
EC: 2.1.1.-
Find proteins for Q9AQ22 (Bradyrhizobium sp. (strain WM9))
Go to UniProtKB:  Q9AQ22
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.010α = 90.00
b = 143.300β = 90.00
c = 75.850γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
MAR345dtbdata collection
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance