5JE1

Crystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) and toxoflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Burkholderia glumae ToxA Is a Dual-Specificity Methyltransferase That Catalyzes the Last Two Steps of Toxoflavin Biosynthesis.

Fenwick, M.K.Philmus, B.Begley, T.P.Ealick, S.E.

(2016) Biochemistry 55: 2748-2759

  • DOI: 10.1021/acs.biochem.6b00167
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toxoflavin is a major virulence factor of the rice pathogen Burkholderia glumae. The tox operon of B. glumae contains five putative toxoflavin biosynthetic genes toxABCDE. ToxA is a predicted S-adenosylmethionine-dependent methyltransferase, and toxA ...

    Toxoflavin is a major virulence factor of the rice pathogen Burkholderia glumae. The tox operon of B. glumae contains five putative toxoflavin biosynthetic genes toxABCDE. ToxA is a predicted S-adenosylmethionine-dependent methyltransferase, and toxA knockouts of B. glumae are less virulent in plant infection models. In this study, we show that ToxA performs two consecutive methylations to convert the putative azapteridine intermediate, 1,6-didemethyltoxoflavin, to toxoflavin. In addition, we report a series of crystal structures of ToxA complexes that reveals the molecular basis of the dual methyltransferase activity. The results suggest sequential methylations with initial methylation at N6 of 1,6-didemethyltoxoflavin followed by methylation at N1. The two azapteridine orientations that position N6 or N1 for methylation are coplanar with a 140° rotation between them. The structure of ToxA contains a class I methyltransferase fold having an N-terminal extension that either closes over the active site or is largely disordered. The ordered conformation places Tyr7 at a position of a structurally conserved tyrosine site of unknown function in various methyltransferases. Crystal structures of ToxA-Y7F consistently show a closed active site, whereas structures of ToxA-Y7A consistently show an open active site, suggesting that the hydroxyl group of Tyr7 plays a role in opening and closing the active site during the multistep reaction.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methyl transferase
A, B
247Burkholderia glumaeMutation(s): 0 
Gene Names: toxA
Find proteins for Q9LBJ0 (Burkholderia glumae)
Go to UniProtKB:  Q9LBJ0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
TOF
Query on TOF

Download SDF File 
Download CCD File 
A, B
1,6-dimethylpyrimido[5,4-e][1,2,4]triazine-5,7(1H,6H)-dione
Toxoflavin
C7 H7 N5 O2
SLGRAIAQIAUZAQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.699α = 90.00
b = 45.567β = 98.98
c = 74.907γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM73220
Robert A. Welch FoundationUnited StatesA-0034
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103403
Department of Energy (United States)United StatesDE-AC02-06CH11357
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103485

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Structure summary