2JDC

Glyphosate N-acetyltransferase bound to oxidized COA and sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Molecular Basis of Glyphosate Resistance by an Optimized Microbial Acetyltransferase.

Siehl, D.L.Castle, L.A.Gorton, R.Keenan, R.J.

(2007) J.Biol.Chem. 282: 11446

  • DOI: 10.1074/jbc.M610267200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GAT is an N-acetyltransferase from Bacillus licheniformis that was optimized by gene shuffling for acetylation of the broad spectrum herbicide, glyphosate, forming the basis of a novel mechanism of glyphosate tolerance in transgenic plants (Castle, L ...

    GAT is an N-acetyltransferase from Bacillus licheniformis that was optimized by gene shuffling for acetylation of the broad spectrum herbicide, glyphosate, forming the basis of a novel mechanism of glyphosate tolerance in transgenic plants (Castle, L. A., Siehl, D. L., Gorton, R., Patten, P. A., Chen, Y. H., Bertain, S., Cho, H. J., Duck, N., Wong, J., Liu, D., and Lassner, M. W. (2004) Science 304, 1151-1154). The 1.6-A resolution crystal structure of an optimized GAT variant in ternary complex with acetyl coenzyme A and a competitive inhibitor, 3-phosphoglyerate, defines GAT as a member of the GCN5-related family of N-acetyltransferases. Four active site residues (Arg-21, Arg-73, Arg-111, and His-138) contribute to a positively charged substrate-binding site that is conserved throughout the GAT subfamily. Structural and kinetic data suggest that His-138 functions as a catalytic base via substrate-assisted deprotonation of the glyphosate secondary amine, whereas another active site residue, Tyr-118, functions as a general acid. Although the physiological substrate is unknown, native GAT acetylates D-2-amino-3-phosphonopropionic acid with a kcat/Km of 1500 min-1 mM-1. Kinetic data show preferential binding of short analogs to native GAT and progressively better binding of longer analogs to optimized variants. Despite a 200-fold increase in kcat and a 5.4-fold decrease in Km for glyphosate, only 4 of the 21 substitutions present in R7 GAT lie in the active site. Single-site revertants constructed at these positions suggest that glyphosate binding is optimized through substitutions that increase the size of the substrate-binding site. The large improvement in kcat is likely because of the cooperative effects of additional substitutions located distal to the active site.


    Organizational Affiliation

    Pioneer Hi-Bred International, Redwood City, California 94063, USA. dan.siehl@pioneer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYPHOSATE N-ACETYLTRANSFERASE
A
146Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)Mutation(s): 0 
Gene Names: yitI
Find proteins for Q65LG7 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46))
Go to UniProtKB:  Q65LG7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CAO
Query on CAO

Download SDF File 
Download CCD File 
A
OXIDIZED COENZYME A
C21 H36 N7 O17 P3 S
HWMGJMKHOJKGLQ-IBOSZNHHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CAOKi: 9000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.056α = 90.00
b = 48.911β = 103.54
c = 46.461γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Data collection, Database references, Derived calculations, Other, Source and taxonomy, Version format compliance