1TUV

Crystal structure of YgiN in complex with menadione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Evidence for an Enzymatic Quinone Redox Cycle in Escherichia coli: IDENTIFICATION OF A NOVEL QUINOL MONOOXYGENASE

Adams, M.A.Jia, Z.

(2005) J.Biol.Chem. 280: 8358-8363

  • DOI: 10.1074/jbc.M412637200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Naturally synthesized quinones perform a variety of important cellular functions. Escherichia coli produce both ubiquinone and menaquinone, which are involved in electron transport. However, semiquinone intermediates produced during the one-electron ...

    Naturally synthesized quinones perform a variety of important cellular functions. Escherichia coli produce both ubiquinone and menaquinone, which are involved in electron transport. However, semiquinone intermediates produced during the one-electron reduction of these compounds, as well as through auto-oxidation of the hydroxyquinone product, generate reactive oxygen species that stress the cell. Here, we present the crystal structure of YgiN, a protein of hitherto unknown function. The three-dimensional fold of YgiN is similar to that of ActVA-Orf6 monooxygenase, which acts on hydroxyquinone substrates. YgiN shares a promoter with "modulator of drug activity B," a protein with activity similar to that of mammalian DT-diaphorase capable of reducing mendione. YgiN was able to reoxidize menadiol, the product of the "modulator of drug activity B" (MdaB) enzymatic reaction. We therefore refer to YgiN as quinol monooxygenase. Modulator of drug activity B is reported to be involved in the protection of cells from reactive oxygen species formed during single electron oxidation and reduction reactions. The enzymatic activities, together with the structural characterization of YgiN, lend evidence to the possible existence of a novel quinone redox cycle in E. coli.


    Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ygiN
A
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ygiN
EC: 1.-.-.-
Find proteins for P0ADU2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADU2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VK3
Query on VK3

Download SDF File 
Download CCD File 
A
MENADIONE
VITAMIN K3; 2-METHYL-1,4-NAPHTHALENEDIONE
C11 H8 O2
MJVAVZPDRWSRRC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.208 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 102.562α = 90.00
b = 102.562β = 90.00
c = 102.562γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2004-06-25 
  • Released Date: 2005-01-11 
  • Deposition Author(s): Adams, M.A., Jia, Z.

Revision History 

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance