2IBN

Crystal structure of Human myo-Inositol Oxygenase (MIOX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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:  

  • 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 c ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol oxygenase
A, B
250Homo sapiensMutation(s): 0 
Gene Names: MIOX (ALDRL6, KSP32, RSOR)
EC: 1.13.99.1
Find proteins for Q9UGB7 (Homo sapiens)
Go to Gene View: MIOX
Go to UniProtKB:  Q9UGB7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
I1N
Query on I1N

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Download CCD File 
A, B
(2S,3R,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
C6 H10 O6
VYEGBDHSGHXOGT-REJXVDBHSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CYS
Query on CYS

Download SDF File 
Download CCD File 
A, B
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.715α = 90.00
b = 55.861β = 116.72
c = 111.516γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
SHARPphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction
ProDCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description