7A0L | pdb_00007a0l

Joint neutron/X-ray room temperature structure of perdeuterated Aspergillus flavus urate oxidase in complex with the 8-azaxanthine inhibitor and catalytic water bound in the peroxo hole

• PDB DOI: https://doi.org/10.2210/pdb7A0L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aspergillus flavus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-08-09 Released: 2020-12-09 
• Deposition Author(s): McGregor, L., Bui, S., Blakeley, M.P., Steiner, R.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 
  0.109 (Depositor) 
• R-Value Work: 
  0.102 (Depositor), 0.336 (DCC) 
• R-Value Observed: 
  0.102 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.230 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Joint neutron/X-ray crystal structure of a mechanistically relevant complex of perdeuterated urate oxidase and simulations provide insight into the hydration step of catalysis.

McGregor, L., Foldes, T., Bui, S., Moulin, M., Coquelle, N., Blakeley, M.P., Rosta, E., Steiner, R.A.

(2021) IUCrJ 8: 46-59

• PubMed: 33520242 
• DOI: https://doi.org/10.1107/S2052252520013615
• Primary Citation Related Structures: 
  7A0L


• PubMed Abstract: 
  

  Cofactor-independent urate oxidase (UOX) is an ∼137 kDa tetrameric enzyme essential for uric acid (UA) catabolism in many organisms. UA is first oxidized by O ₂ to de-hydro-isourate (DHU) via a peroxo intermediate. DHU then undergoes hydration to 5-hy-droxy-isourate (5HIU). At different stages of the reaction both catalytic O ₂ and water occupy the 'peroxo hole' above the organic substrate. Here, high-resolution neutron/X-ray crystallographic analysis at room temperature has been integrated with molecular dynamics simulations to investigate the hydration step of the reaction. The joint neutron/X-ray structure of perdeuterated Aspergillus flavus UOX in complex with its 8-azaxanthine (8AZA) inhibitor shows that the catalytic water molecule (W1) is present in the peroxo hole as neutral H ₂ O, oriented at 45° with respect to the ligand. It is stabilized by Thr57 and Asn254 on different UOX protomers as well as by an O-H⋯π interaction with 8AZA. The active site Lys10-Thr57 dyad features a charged Lys10-NH ₃ ⁺ side chain engaged in a strong hydrogen bond with Thr57 ^OG1 , while the Thr57 ^OG1-HG1 bond is rotationally dynamic and oriented toward the π system of the ligand, on average. Our analysis offers support for a mechanism in which W1 performs a nucleophilic attack on DHU ^C5 with Thr57 ^HG1 central to a Lys10-assisted proton-relay system. Room-temperature crystallography and simulations also reveal conformational heterogeneity for Asn254 that modulates W1 stability in the peroxo hole. This is proposed to be an active mechanism to facilitate W1/O ₂ exchange during catalysis.

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Organizational Affiliation: 
• Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, United Kingdom.
Large Scale Structures Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France.
Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.
Department of Physics and Astronomy, University College, London WC1E 6BT, United Kingdom.
Life Sciences Group, Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Cedex 9, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.46 kDa 
• Atom Count: 2,974 
• Modeled Residue Count: 296 
• Deposited Residue Count: 303 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A	302	Aspergillus flavus	Mutation(s): 0  Gene Names: uaZ, uox EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511  Go to UniProtKB:  Q00511

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZA (Subject of Investigation/LOI)	B [auth A]	8-AZAXANTHINE C4 H3 N5 O2 KVGVQTOQSNJTJI-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free:  0.109 (Depositor) 
• R-Value Work:  0.102 (Depositor), 0.336 (DCC) 
• R-Value Observed: 0.102 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.230 (Depositor) 
• R-Value Work:  0.215 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.628	α = 90
b = 96.13	β = 90
c = 105.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
LAUEGEN	data processing
DIALS	data processing
SCALA	data scaling
PHENIX	phasing
xia2	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): McGregor, L., Bui, S., Blakeley, M.P., Steiner, R.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P000169/1

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary