7F2W | pdb_00007f2w

TbUox in complex with uric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and biochemical insights into a hyperthermostable urate oxidase from Thermobispora bispora for hyperuricemia and gout therapy.

Chiu, Y.C.Hsu, T.S.Huang, C.Y.Hsu, C.H.

(2021) Int J Biol Macromol 188: 914-923

  • DOI: https://doi.org/10.1016/j.ijbiomac.2021.08.081
  • Primary Citation Related Structures: 
    7F2V, 7F2W

  • PubMed Abstract: 

    Microbial urate oxidase has emerged as a potential source of therapeutic properties for hyperuricemia in arthritic gout and renal disease. The thermostability and long-term thermal tolerance of the enzyme need to be established to prolong its therapeutic effects. Here, we present the biochemical and structural aspects of a hyperthermostable urate oxidase (TbUox) from the thermophilic microorganism Thermobispora bispora. Enzymatic characterization of TbUox revealed that it was active over a wide range of temperatures, from 30 to 70 °C, with optimal activity at 65 °C and pH 8.0, which suggests its applicability under physiological conditions. Moreover, TbUox exhibits high thermostability from 10 to 65 °C, with Tm of 70.3 °C and near-neutral pH stability from pH 7.0 to 8.0 and high thermal tolerance. The crystal structures of TbUox revealed a distinct feature of the C-terminal loop extensions that may help with protein stability via inter-subunit interactions. In addition, the high thermal tolerance of TbUox may be contributed by the extensive inter-subunit contacts via salt bridges, hydrogen bonds, and hydrophobic interactions. The findings in this study provide a molecular basis for the thermophilic TbUox urate oxidase for application in hyperuricemia and gout therapy.


  • Organizational Affiliation
    • Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 68.62 kDa 
  • Atom Count: 5,231 
  • Modeled Residue Count: 600 
  • Deposited Residue Count: 608 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uricase
A, B
304Thermobispora bispora DSM 43833Mutation(s): 0 
Gene Names: Tbis_2592
EC: 1.7.3.3
UniProt
Find proteins for D6Y599 (Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / KCTC 9307 / NBRC 14880 / R51))
Explore D6Y599 
Go to UniProtKB:  D6Y599
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6Y599
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.362α = 90
b = 146.362β = 90
c = 132.407γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-2113-M- 002-003
Ministry of Science and Technology (MoST, Taiwan)Taiwan109-2628-B-002-037
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2113-M-002-011
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2628-B-002-013

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description