7KCN | pdb_00007kcn

Reconstructed ancestor of HIUases and Transthyretins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KCN

This is version 1.3 of the entry. See complete history

Literature

Reenacting the Birth of a Function: Functional Divergence of HIUases and Transthyretins as Inferred by Evolutionary and Biophysical Studies.

Carrijo de Oliveira, L.Figueiredo Costa, M.A.Goncalves Pedersolli, N.Heleno Batista, F.A.Migliorini Figueira, A.C.Salgado Ferreira, R.Alves Pinto Nagem, R.Alves Nahum, L.Bleicher, L.

(2021) J Mol Evol 89: 370-383

  • DOI: https://doi.org/10.1007/s00239-021-10010-8
  • Primary Citation Related Structures: 
    7KCN, 7KJJ

  • PubMed Abstract: 

    Transthyretin was discovered in the 1940s, named after its ability to bind thyroid hormones and retinol. In the genomic era, transthyretins were found to be part of a larger family with homologs of no obvious function, then called transthyretin-related proteins. Thus, it was proposed that the transthyretin gene could be the result of gene duplication of an ancestral of this newly identified homolog, later found out to be an enzyme involved in uric acid degradation, then named HIUase (5-hydroxy-isourate hydrolase). Here, we sought to re-enact the evolutionary history of this protein family by reconstructing, from a phylogeny inferred from 123 vertebrate sequences, three ancestors corresponding to key moments in their evolution-before duplication; the common transthyretin ancestor after gene duplication and the common ancestor of Eutheria transthyretins. Experimental and computational characterization showed the reconstructed ancestor before duplication was unable to bind thyroxine and likely presented the modern HIUase reaction mechanism, while the substitutions after duplication prevented that activity and were enough to provide stable thyroxine binding, as confirmed by calorimetry and x-ray diffraction. The Eutheria transthyretin ancestor was less prone to characterization, but limited data suggested thyroxine binding as expected. Sequence/structure analysis suggests an early ability to bind the Retinol Binding Protein. We solved the X-ray structures from the two first ancestors, the first at 1.46 resolution, the second at 1.55 resolution with well-defined electron density for thyroxine, providing a useful tool for the understanding of structural adaptation from enzyme to hormone distributor.


  • Organizational Affiliation
    • Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.

Macromolecule Content 

  • Total Structure Weight: 27.99 kDa 
  • Atom Count: 2,144 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HIUase-TTR ancestor
A, B
122synthetic constructMutation(s): 0 
EC: 3.5.2.17
UniProt
Find proteins for A0A3B3I7P0 (Oryzias latipes)
Explore A0A3B3I7P0 
Go to UniProtKB:  A0A3B3I7P0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B3I7P0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.03α = 90
b = 67.03β = 90
c = 116.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
PHENIXphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Coordination for the Improvement of Higher Education PersonnelBrazil23038.010059/2013-15 AUXPE 3379/2013

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-08-18
    Changes: Database references, Source and taxonomy
  • Version 1.3: 2024-05-22
    Changes: Data collection