3TNZ

Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C217A, C239A bound to FMN and mono-iodotyrosine (MIT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Expression of a soluble form of iodotyrosine deiodinase for active site characterization by engineering the native membrane protein from Mus musculus.

Buss, J.M.McTamney, P.M.Rokita, S.E.

(2012) Protein Sci. 21: 351-361

  • DOI: 10.1002/pro.2020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Reductive deiodination is critical for thyroid function and represents an unusual exception to the more common oxidative and hydrolytic mechanisms of dehalogenation in mammals. Studies on the reductive processes have been limited by a lack of conveni ...

    Reductive deiodination is critical for thyroid function and represents an unusual exception to the more common oxidative and hydrolytic mechanisms of dehalogenation in mammals. Studies on the reductive processes have been limited by a lack of convenient methods for heterologous expression of the appropriate proteins in large scale. The enzyme responsible for iodide salvage in the thyroid, iodotyrosine deodinase, is now readily generated after engineering its gene from Mus musculus. High expression of a truncated derivative lacking the membrane domain at its N-terminal was observed in Sf9 cells, whereas expression in Pichia pastoris remained low despite codon optimization. Ultimately, the desired expression in Escherichia coli was achieved after replacing the two conserved Cys residues of the deiodinase with Ala and fusing the resulting protein to thioredoxin. This final construct provided abundant enzyme for crystallography and mutagenesis. Utility of the E. coli system was demonstrated by examining a set of active site residues critical for binding to the zwitterionic portion of substrate.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742-2021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iodotyrosine dehalogenase 1
A, B
259Mus musculusMutation(s): 2 
Gene Names: Iyd (Dehal1)
EC: 1.21.1.1
Find proteins for Q9DCX8 (Mus musculus)
Go to UniProtKB:  Q9DCX8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
IYR
Query on IYR

Download SDF File 
Download CCD File 
A, B
3-IODO-TYROSINE
C9 H10 I N O3
UQTZMGFTRHFAAM-ZETCQYMHSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IYRKd: 90 nM (86) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.171 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 108.986α = 90.00
b = 108.986β = 90.00
c = 49.399γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CCP4phasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data collection
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2012-04-04
    Type: Database references