3BXD

Crystal structure of Mouse Myo-inositol oxygenase (re-refined)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:2HUO


Literature

Structural and biophysical characterization of human myo-inositol oxygenase.

Thorsell, A.G.Persson, C.Voevodskaya, N.Busam, R.D.Hammarstrom, M.Graslund, S.Graslund, A.Hallberg, B.M.

(2008) J Biol Chem 283: 15209-15216

  • DOI: 10.1074/jbc.M800348200
  • Primary Citation of Related Structures:  
    3BXD, 2IBN

  • PubMed Abstract: 
  • Altered inositol metabolism is implicated in a number of diabetic complications. The first committed step in mammalian inositol catabolism is performed by myo-inositol oxygenase (MIOX), which catalyzes a unique four-electron dioxygen-dependent ring cleavage of myo-inositol to D-glucuronate ...

    Altered inositol metabolism is implicated in a number of diabetic complications. The first committed step in mammalian inositol catabolism is performed by myo-inositol oxygenase (MIOX), which catalyzes a unique four-electron dioxygen-dependent ring cleavage of myo-inositol to D-glucuronate. Here, we present the crystal structure of human MIOX in complex with myo-inosose-1 bound in a terminal mode to the MIOX diiron cluster site. Furthermore, from biochemical and biophysical results from N-terminal deletion mutagenesis we show that the N terminus is important, through coordination of a set of loops covering the active site, in shielding the active site during catalysis. EPR spectroscopy of the unliganded enzyme displays a two-component spectrum that we can relate to an open and a closed active site conformation. Furthermore, based on site-directed mutagenesis in combination with biochemical and biophysical data, we propose a novel role for Lys(127) in governing access to the diiron cluster.


    Related Citations: 
    • Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.
      Brown, P.M., Caradoc-Davies, T.T., Dickson, J.M., Cooper, G.J., Loomes, K.M., Baker, E.N.
      (2006) Proc Natl Acad Sci U S A 103: 15032

    Organizational Affiliation

    Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, SE-171 77 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
INOSITOL OXYGENASEA289Mus musculusMutation(s): 0 
Gene Names: MioxAldrl6Rsor
EC: 1.13.99.1
UniProt
Find proteins for Q9QXN5 (Mus musculus)
Explore Q9QXN5 
Go to UniProtKB:  Q9QXN5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
INS
Query on INS

Download Ideal Coordinates CCD File 
E [auth A]1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
F [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
OH
Query on OH

Download Ideal Coordinates CCD File 
D [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
INSKi:  62000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.6α = 90
b = 77.2β = 90
c = 85.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-01-13 
  • Released Date: 2008-02-05 
  • Deposition Author(s): Hallberg, B.M.

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-12
    Changes: Other
  • Version 1.3: 2017-10-25
    Changes: Refinement description