6XLT | pdb_00006xlt

The 1.48 Angstrom crystal structure of evolved galactose oxidase variant A3.E7

  • Classification: OXIDOREDUCTASE
  • Organism(s): Fusarium graminearum
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2020-06-29 Released: 2021-02-03 
  • Deposition Author(s): Liu, A., Li, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.169 (Depositor), 0.175 (DCC) 
  • R-Value Work: 
    0.148 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Formation of Monofluorinated Radical Cofactor in Galactose Oxidase through Copper-Mediated C-F Bond Scission.

Li, J.Davis, I.Griffith, W.P.Liu, A.

(2020) J Am Chem Soc 142: 18753-18757

  • DOI: https://doi.org/10.1021/jacs.0c08992
  • Primary Citation Related Structures: 
    6XLR, 6XLS, 6XLT

  • PubMed Abstract: 

    Galactose oxidase (GAO) contains a Cu(II)-ligand radical cofactor. The cofactor, which is autocatalytically generated through the oxidation of the copper, consists of a cysteine-tyrosine radical (Cys-Tyr ) as a copper ligand. The formation of the cross-linked thioether bond is accompanied by a C-H bond scission on Tyr272 with few details known thus far. Here, we report the genetic incorporation of 3,5-dichlorotyrosine (Cl 2 -Tyr) and 3,5-difluorotyrosine (F 2 -Tyr) to replace Tyr272 in the GAO V previously optimized for expression through directed evolution. The proteins with an unnatural tyrosine residue are catalytically competent. We determined the high-resolution crystal structures of the GAO V , Cl 2 -Tyr272, and F 2 -Tyr272 incorporated variants at 1.48, 1.23, and 1.80 Å resolution, respectively. The structural data showed only one halogen remained in the cofactor, indicating that an oxidative carbon-chlorine/fluorine bond scission has occurred during the autocatalytic process of cofactor biogenesis. Using hydroxyurea as a radical scavenger, the spin-coupled hidden Cu(II) was observed by EPR spectroscopy. Thus, the structurally defined catalytic center with genetic unnatural tyrosine substitution is in the radical containing form as in the wild-type, i.e., Cu(II)-(Cl-Tyr -Cys) or Cu(II)-(F-Tyr -Cys). These findings illustrate a previously unobserved C-F/C-Cl bond cleavage in biology mediated by a mononuclear copper center.


  • Organizational Affiliation
    • Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States.

Macromolecule Content 

  • Total Structure Weight: 70.12 kDa 
  • Atom Count: 5,718 
  • Modeled Residue Count: 639 
  • Deposited Residue Count: 648 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactose oxidase648Fusarium graminearumMutation(s): 5 
Gene Names: GAOA
EC: 1.1.3.9
UniProt
Find proteins for P0CS93 (Gibberella zeae)
Explore P0CS93 
Go to UniProtKB:  P0CS93
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CS93
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.169 (Depositor), 0.175 (DCC) 
  • R-Value Work:  0.148 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.282α = 90
b = 89.12β = 117.82
c = 86.162γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2021-02-03 
  • Deposition Author(s): Liu, A., Li, J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988
National Science Foundation (NSF, United States)United StatesCHE-1808637

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary