5T7E

Crystal structure of Streptomyces hygroscopicus Bialaphos Resistance (BAR) protein in complex with Coenzyme A and L-phosphinothricin

  • Classification: TRANSFERASE
  • Organism(s): Streptomyces hygroscopicus
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2016-09-04 Released: 2017-06-07 
  • Deposition Author(s): Christ, B., Weng, J.K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States), Swiss National Science Foundation, Pew Scholar Program in the Biomedical Sciences, Searle Scholars Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Non-specific activities of the major herbicide-resistance gene BAR.

Christ, B.Hochstrasser, R.Guyer, L.Francisco, R.Aubry, S.Hortensteiner, S.Weng, J.K.

(2017) Nat Plants 3: 937-945

  • DOI: https://doi.org/10.1038/s41477-017-0061-1
  • Primary Citation of Related Structures:  
    5T7D, 5T7E

  • PubMed Abstract: 

    Bialaphos resistance (BAR) and phosphinothricin acetyltransferase (PAT) genes, which convey resistance to the broad-spectrum herbicide phosphinothricin (also known as glufosinate) via N-acetylation, have been globally used in basic plant research and genetically engineered crops 1-4 . Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids 1 , indirect effects of BAR-containing transgenes in planta, including modified amino acid levels, have been seen but without the identification of their direct causes 5,6 . Combining metabolomics, plant genetics and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced non-specific activities compared with its wild-type counterpart in vivo. The transgenic expression of enzymes can result in unintended off-target metabolism arising from enzyme promiscuity. Understanding such phenomena at the mechanistic level can facilitate the design of maximally insulated systems featuring heterologously expressed enzymes.


  • Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphinothricin N-acetyltransferase
A, B, C, D
189Streptomyces hygroscopicusMutation(s): 0 
Gene Names: bar
EC: 2.3.1.183
UniProt
Find proteins for P16426 (Streptomyces hygroscopicus)
Explore P16426 
Go to UniProtKB:  P16426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16426
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
BNG
Query on BNG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
nonyl beta-D-glucopyranoside
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
PPQ
Query on PPQ

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
N [auth D]
PHOSPHINOTHRICIN
C5 H12 N O4 P
IAJOBQBIJHVGMQ-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.18α = 90
b = 66.11β = 103.06
c = 86.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR029205
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
Swiss National Science FoundationSwitzerlandP2ZHP3_155258
Pew Scholar Program in the Biomedical SciencesUnited States--
Searle Scholars ProgramUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2022-04-13
    Changes: Author supporting evidence, Database references, Structure summary
  • Version 1.6: 2024-05-22
    Changes: Data collection