4TTC

Crystal structure of homo sapiens IODOTYROSINE DEIODINASE bound to FMN and mono-iodotyrosine (MIT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Switch between One- and Two-electron Chemistry of the Human Flavoprotein Iodotyrosine Deiodinase Is Controlled by Substrate.

Hu, J.Chuenchor, W.Rokita, S.E.

(2015) J Biol Chem 290: 590-600

  • DOI: 10.1074/jbc.M114.605964
  • Primary Citation of Related Structures:  
    4TTB, 4TTC

  • PubMed Abstract: 
  • Reductive dehalogenation is not typical of aerobic organisms but plays a significant role in iodide homeostasis and thyroid activity. The flavoprotein iodotyrosine deiodinase (IYD) is responsible for iodide salvage by reductive deiodination of the io ...

    Reductive dehalogenation is not typical of aerobic organisms but plays a significant role in iodide homeostasis and thyroid activity. The flavoprotein iodotyrosine deiodinase (IYD) is responsible for iodide salvage by reductive deiodination of the iodotyrosine derivatives formed as byproducts of thyroid hormone biosynthesis. Heterologous expression of the human enzyme lacking its N-terminal membrane anchor has allowed for physical and biochemical studies to identify the role of substrate in controlling the active site geometry and flavin chemistry. Crystal structures of human IYD and its complex with 3-iodo-l-tyrosine illustrate the ability of the substrate to provide multiple interactions with the isoalloxazine system of FMN that are usually provided by protein side chains. Ligand binding acts to template the active site geometry and significantly stabilize the one-electron-reduced semiquinone form of FMN. The neutral form of this semiquinone is observed during reductive titration of IYD in the presence of the substrate analog 3-fluoro-l-tyrosine. In the absence of an active site ligand, only the oxidized and two-electron-reduced forms of FMN are detected. The pH dependence of IYD binding and turnover also supports the importance of direct coordination between substrate and FMN for productive catalysis.


    Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742 and Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218 rokita@jhu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iodotyrosine dehalogenase 1ABCDEF265Homo sapiensMutation(s): 0 
Gene Names: IYDC6orf71DEHAL1
EC: 1.22.1.1 (PDB Primary Data), 1.21.1.1 (UniProt)
Find proteins for Q6PHW0 (Homo sapiens)
Explore Q6PHW0 
Go to UniProtKB:  Q6PHW0
NIH Common Fund Data Resources
PHAROS  Q6PHW0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B, C, D, E, F
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
IYR
Query on IYR

Download CCD File 
A, B, C, D, E, F
3-IODO-TYROSINE
C9 H10 I N O3
UQTZMGFTRHFAAM-ZETCQYMHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IYRKd:  90   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.747α = 90
b = 104.747β = 90
c = 303.338γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK084186

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence