5K1M

Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with p-methoxyphenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural dissection of Shewanella oneidensis old yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands.

Elegheert, J.Brige, A.Van Beeumen, J.Savvides, S.N.

(2017) FEBS Lett 591: 3391-3401

  • DOI: https://doi.org/10.1002/1873-3468.12833
  • Primary Citation of Related Structures:  
    4B5N, 5K0R, 5K1K, 5K1M, 5K1Q, 5K1U, 5K1W

  • PubMed Abstract: 

    Shewanella oneidensis, a Gram-negative γ-proteobacterium with an extensive redox capacity, possesses four old yellow enzyme (OYE) homologs. Of these, Shewanella yellow enzyme 4 (SYE4) is implicated in resistance to oxidative stress. Here, we present a series of high-resolution crystal structures for SYE4 in the oxidized and reduced states, and in complex with phenolic ligands and the nitro-aromatic explosive picric acid. The structures unmask new features, including the identification of a binding platform for long-chain hydrophobic molecules. Furthermore, we present the first structural observation of a hydride-Meisenheimer complex of picric acid with a flavoenzyme. Overall, our study exposes the binding promiscuity of SYE4 toward a variety of electrophilic substrates and is consistent with a general detoxification function for SYE4.


  • Organizational Affiliation

    Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Department of Biochemistry and Microbiology, Ghent University, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H:flavin oxidoreductase Sye4355Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: sye4SO_3392
EC: 1.5.1.30
UniProt
Find proteins for Q8EBV3 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EBV3 
Go to UniProtKB:  Q8EBV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EBV3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.18α = 90
b = 54.83β = 90
c = 103.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description