6E1J

Crystal Structure of Methylthioalkylmalate Synthase (BjuMAM1.1) from Brassica juncea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates.

Kumar, R.Lee, S.G.Augustine, R.Reichelt, M.Vassao, D.G.Palavalli, M.H.Allen, A.Gershenzon, J.Jez, J.M.Bisht, N.C.

(2019) Plant Cell 31: 1633-1647

  • DOI: 10.1105/tpc.19.00046
  • Primary Citation of Related Structures:  
    6E1J

  • PubMed Abstract: 
  • The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis ...

    The globally cultivated Brassica species possess diverse aliphatic glucosinolates, which are important for plant defense and animal nutrition. The committed step in the side chain elongation of methionine-derived aliphatic glucosinolates is catalyzed by methylthioalkylmalate synthase, which likely evolved from the isopropylmalate synthases of leucine biosynthesis. However, the molecular basis for the evolution of methylthioalkylmalate synthase and its generation of natural product diversity in Brassica is poorly understood. Here, we show that Brassica genomes encode multiple methylthioalkylmalate synthases that have differences in expression profiles and 2-oxo substrate preferences, which account for the diversity of aliphatic glucosinolates across Brassica accessions. Analysis of the 2.1 Å resolution x-ray crystal structure of Brassica juncea methylthioalkylmalate synthase identified key active site residues responsible for controlling the specificity for different 2-oxo substrates and the determinants of side chain length in aliphatic glucosinolates. Overall, these results provide the evolutionary and biochemical foundation for the diversification of glucosinolate profiles across globally cultivated Brassica species, which could be used with ongoing breeding strategies toward the manipulation of beneficial glucosinolate compounds for animal health and plant protection.


    Organizational Affiliation

    National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India jjez@wustl.edu ncbisht@nipgr.ac.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-isopropylmalate synthase, A genome specific 1A, B505Brassica junceaMutation(s): 0 
Gene Names: gsl-elong-A1
UniProt
Find proteins for C5J4P1 (Brassica juncea)
Explore C5J4P1 
Go to UniProtKB:  C5J4P1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
F [auth A], I [auth B]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
KMT
Query on KMT

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]4-(METHYLSULFANYL)-2-OXOBUTANOIC ACID
C5 H8 O3 S
SXFSQZDSUWACKX-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], G [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.749α = 90
b = 90.277β = 107.75
c = 93.975γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
MOLREPphasing
Cootmodel building
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-07-09 
  • Released Date: 2019-05-08 
  • Deposition Author(s): Lee, S.G., Jez, J.M.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-MCB-1614539

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence