2IBN

Crystal structure of Human myo-Inositol Oxygenase (MIOX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.5 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: https://doi.org/10.1074/jbc.M800348200
  • Primary Citation of Related Structures:  
    2IBN, 3BXD

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol oxygenase
A, B
250Homo sapiensMutation(s): 0 
EC: 1.13.99.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGB7 (Homo sapiens)
Explore Q9UGB7 
Go to UniProtKB:  Q9UGB7
PHAROS:  Q9UGB7
GTEx:  ENSG00000100253 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGB7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I1N
Query on I1N

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
(2S,3R,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
C6 H10 O6
VYEGBDHSGHXOGT-REJXVDBHSA-N
CYS
Query on CYS

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-REOHCLBHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
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: 1.50 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.715α = 90
b = 55.861β = 116.72
c = 111.516γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted I1NClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-10-30
    Changes: Structure summary