7VQK

Catalytic manifolds of a FMN-dependent oxidoreductase RubE7, expanding the functional diversity of the flavoenzyme superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

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This is version 2.0 of the entry. See complete history


Literature

Characterization of Multifunctional and Non-stereoselective Oxidoreductase RubE7/IstO, Expanding the Functional Diversity of the Flavoenzyme Superfamily.

Yan, Y.Yu, Z.Zhong, W.Hou, X.Tao, Q.Cao, M.Wang, L.Cai, X.Rao, Y.Huang, S.X.

(2022) Angew Chem Int Ed Engl 61: e202200189-e202200189

  • DOI: https://doi.org/10.1002/anie.202200189
  • Primary Citation of Related Structures:  
    7VQK

  • PubMed Abstract: 

    Flavin-dependent enzymes enable a broad range of redox transformations and generally act as monofunctional and stereoselective catalysts. Herein, we report the investigation of a multifunctional and non-stereoselective FMN-dependent oxidoreductase RubE7 from the rubrolone biosynthetic pathway. Our study outlines a single RubE7-catalysed sequential reduction of three spatially distinct bonds in a tropolone ring and a reversible double-bond reduction and dehydrogenation. The crystal structure of IstO (a RubE7 homologue) with 2.0 Å resolution reveals the location of the active site at the interface of two monomers, and the size of active site is large enough to permit both flipping and free rotation of the substrate, resulting in multiple nonselective reduction reactions. Molecular docking and site mutation studies demonstrate that His106 is oriented towards the substrate and is important for the reverse dehydrogenation reaction.


  • Organizational Affiliation

    State Key Laboratory of Phytochemistry and Plant Resources in West China, CAS Center for Excellence in Molecular Plant Sciences, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FMN-dependent oxidoreductase IstO
A, B
199Streptomyces sp. KIB-H033Mutation(s): 0 
Gene Names: rutE2EES42_11050
EC: 1.1.1.298
UniProt
Find proteins for A0A3N6GWZ7 (Streptomyces sp. ADI95-17)
Explore A0A3N6GWZ7 
Go to UniProtKB:  A0A3N6GWZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3N6GWZ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.701α = 90
b = 54.41β = 97.367
c = 69.621γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB27020205

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 2.0: 2023-06-07
    Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary