5K1W

Crystal structure of oxidized Shewanella Yellow Enzyme 4 (SYE4) in complex with trinitrophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1002/1873-3468.12833
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    Ablynx NV, Zwijnaarde, Belgium.,Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE), Department of Biochemistry and Microbiology, Ghent University, Belgium.,VIB-UGent Center for Inflammation Research (IRC), Ghent University, Zwijnaarde, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H:flavin oxidoreductase Sye4
A
355Shewanella oneidensis (strain MR-1)Mutation(s): 0 
Gene Names: sye4
EC: 1.5.1.30
Find proteins for Q8EBV3 (Shewanella oneidensis (strain MR-1))
Go to UniProtKB:  Q8EBV3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
8K6
Query on 8K6

Download SDF File 
Download CCD File 
A
Octadecane
N-Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
 Ligand Interaction
TNF
Query on TNF

Download SDF File 
Download CCD File 
A
PICRIC ACID
2,4,6-TRINITROPHENOL
C6 H3 N3 O7
OXNIZHLAWKMVMX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.180α = 90.00
b = 54.770β = 90.00
c = 103.500γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references