6GNR

Crystal Structure Of Sea Bream Transthyretin in complex with 2-(3-chloro-2-methylanilino)pyridine-3-carboxylic acid (Clonixin)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

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This is version 1.3 of the entry. See complete history


Literature

Interspecies Variation between Fish and Human Transthyretins in Their Binding of Thyroid-Disrupting Chemicals.

Zhang, J.Grundstrom, C.Brannstrom, K.Iakovleva, I.Lindberg, M.Olofsson, A.Andersson, P.L.Sauer-Eriksson, A.E.

(2018) Environ Sci Technol 52: 11865-11874

  • DOI: 10.1021/acs.est.8b03581
  • Primary Citation of Related Structures:  
    6GNW, 6GNM, 6GNP, 6GNO, 6GNR, 6GOO, 6GON, 6GR7, 6GRP

  • PubMed Abstract: 
  • Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis ...

    Thyroid-disrupting chemicals (TDCs) are xenobiotics that can interfere with the endocrine system and cause adverse effects in organisms and their offspring. TDCs affect both the thyroid gland and regulatory enzymes associated with thyroid hormone homeostasis. Transthyretin (TTR) is found in the serum and cerebrospinal fluid of vertebrates, where it transports thyroid hormones. Here, we explored the interspecies variation in TDC binding to human and fish TTR (exemplified by Gilthead seabream ( Sparus aurata)). The in vitro binding experiments showed that TDCs bind with equal or weaker affinity to seabream TTR than to the human TTR, in particular, the polar TDCs (>500-fold lower affinity). Crystal structures of the seabream TTR-TDC complexes revealed that all TDCs bound at the thyroid binding sites. However, amino acid substitution of Ser117 in human TTR to Thr117 in seabream prevented polar TDCs from binding deep in the hormone binding cavity, which explains their low affinity to seabream TTR. Molecular dynamics and in silico alanine scanning simulation also suggested that the protein backbone of seabream TTR is more rigid than the human one and that Thr117 provides fewer electrostatic contributions than Ser117 to ligand binding. This provides an explanation for the weaker affinities of the ligands that rely on electrostatic interactions with Thr117. The lower affinities of TDCs to fish TTR, in particular the polar ones, could potentially lead to milder thyroid-related effects in fish.


    Related Citations: 
    • Structure-Based Virtual Screening Protocol for in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin.
      Zhang, J., Begum, A., Brannstrom, K., Grundstrom, C., Iakovleva, I., Olofsson, A., Sauer-Eriksson, A.E., Andersson, P.L.
      (2016) Environ Sci Technol 50: 11984

    Organizational Affiliation

    Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TransthyretinA, B135Sparus aurataMutation(s): 0 
UniProt
Find proteins for Q9PTT3 (Sparus aurata)
Explore Q9PTT3 
Go to UniProtKB:  Q9PTT3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6J3 (Subject of Investigation/LOI)
Query on 6J3

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-(3-chloro-2-methylanilino)pyridine-3-carboxylic acid
C13 H11 Cl N2 O2
CLOMYZFHNHFSIQ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6J3 Binding MOAD:  6GNR Kd: 3610 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.678α = 90
b = 59.678β = 90
c = 115.701γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-04-24
    Changes: Data collection, Database references