5AYJ | pdb_00005ayj

Hyperthermostable mutant of Bacillus sp. TB-90 Urate Oxidase - R298C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity

Hibi, T.Kume, A.Kawamura, A.Itoh, T.Fukada, H.Nishiya, Y.

(2016) Biochemistry 55: 724-732

  • DOI: https://doi.org/10.1021/acs.biochem.5b01119
  • Primary Citation Related Structures: 
    5AYJ

  • PubMed Abstract: 

    Bacillus sp. TB-90 urate oxidase (BTUO) is one of the most thermostable homotetrameric enzymes. We previously reported [Hibi, T., et al. (2014) Biochemistry 53, 3879-3888] that specific binding of a sulfate anion induced thermostabilization of the enzyme, because the bound sulfate formed a salt bridge with two Arg298 residues, which stabilized the packing between two β-barrel dimers. To extensively characterize the sulfate-binding site, Arg298 was substituted with cysteine by site-directed mutagenesis. This substitution markedly increased the protein melting temperature by ∼ 20 °C compared with that of the wild-type enzyme, which was canceled by reduction with dithiothreitol. Calorimetric analysis of the thermal denaturation suggested that the hyperstabilization resulted from suppression of the dissociation of the tetramer into the two homodimers. The crystal structure of R298C at 2.05 Å resolution revealed distinct disulfide bond formation between the symmetrically related subunits via Cys298, although the Cβ distance between Arg298 residues of the wild-type enzyme (5.4 Å apart) was too large to predict stable formation of an engineered disulfide cross-link. Disulfide bonding was associated with local disordering of interface loop II (residues 277-300), which suggested that the structural plasticity of the loop allowed hyperstabilization by disulfide formation. Another conformational change in the C-terminal region led to intersubunit hydrogen bonding between Arg7 and Asp312, which probably promoted mutant thermostability. Knowledge of the disulfide linkage of flexible loops at the subunit interface will help in the development of new strategies for enhancing the thermostabilization of multimeric proteins.


  • Organizational Affiliation
    • Department of Bioscience, Fukui Prefectural University , Fukui 910-1195, Japan.

Macromolecule Content 

  • Total Structure Weight: 154.23 kDa 
  • Atom Count: 9,851 
  • Modeled Residue Count: 1,197 
  • Deposited Residue Count: 1,324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uric acid degradation bifunctional protein
A, B, C, D
331Bacillus sp. TB-90Mutation(s): 1 
Gene Names: uao
EC: 1.7.3.3 (PDB Primary Data), 4.1.1.97 (UniProt)
UniProt
Find proteins for Q45697 (Bacillus sp. (strain TB-90))
Explore Q45697 
Go to UniProtKB:  Q45697
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45697
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
F [auth A]
I [auth B]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
I [auth B],
J [auth B],
K [auth B],
N [auth C],
P [auth D]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
MUA

Query on MUA



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
M [auth C],
Q [auth D]
9-METHYL URIC ACID
C6 H6 N4 O3
XJEJWDFDVPDMAS-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
O [auth C],
R [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.861α = 90
b = 142.581β = 90
c = 70.649γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary