8UW4

Crystal structure of hydroxyisourate hydrolase from Herbaspirillum seropedicae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Evolution-based protein engineering: functional switching between transthyretins and 5-hydroxyisourate hydrolases.

Lemos, R.P.Rodrigues, J.T.Portwood, G.de Oliveira, L.C.Gomes Dos Santos, P.H.Costa, M.A.F.Pereira, H.D.Bleicher, L.de Magalhaes, M.T.Q.

(2024) J Biomol Struct Dyn : 1-17

  • DOI: https://doi.org/10.1080/07391102.2024.2440647
  • Primary Citation of Related Structures:  
    8UW4

  • PubMed Abstract: 

    Transthyretin (TTR) is a vertebrate-exclusive transport protein that plays a key role in binding and distributing thyroid hormones. However, its evolutionary origin lies in the duplication of the gene that encoding the enzyme 5-hydroxyisourate hydrolase (HIUase), which is involved in uric acid metabolism. Unlike TTR, HIUase is ubiquitous in both prokaryotes and eukaryotes, with the exception of hominids. Both HIUase and TTR subfamilies form homotetramers, possessing an internal charged cavity between the two dimer pairs. Based on their high degree of structural similarity, we hypothesized that specific in silico substitutions would enable the interconversion between these protein functions. Using an evolution-based approach, we engineered two putative protein sequences, where correlated locally conserved positions from one subfamily representative sequence were substituted by the other, and vice versa. Applying computational modeling techniques, the best models were refined, validated, and their cavity volumes, three-dimensional geometries, propensity to aggregation and electrostatic potentials were analyzed. Molecular dynamics simulations were performed with the reference proteins and the engineered mutants in the bound and unbound states. We demonstrate that the volumes and geometries differ from one another, due to size and physicochemical differences between their ligands. The bound state mutant complexes are stable, and the enzymatic assay demonstrated active new enzymes. Our work suggests that the evolution-based protein engineering approach used has residue-specific resolution to identify locally conserved residues in the sequence of evolutionarily related proteins, such as HIUase and TTR.


  • Organizational Affiliation

    Laboratory for Macromolecular Biophysics - LBM, Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Brazil.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxyisourate hydrolase
A, B, C, D, E
137Herbaspirillum seropedicaeMutation(s): 0 
Gene Names: uraH
EC: 3.5.2.17
UniProt
Find proteins for D8J1G5 (Herbaspirillum seropedicae (strain SmR1))
Explore D8J1G5 
Go to UniProtKB:  D8J1G5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD8J1G5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.286α = 90
b = 102.662β = 94.38
c = 119.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil457851/2014-7
Minas Gerais State Agency for Research and Development (FAPEMIG)BrazilUniversal APQ-01898-22

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references, Structure summary