4N9V | pdb_00004n9v

High resolution x-ray structure of urate oxidase in complex with 8-azaxanthine

PDB DOI: https://doi.org/10.2210/pdb4N9V/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus flavus
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2013-10-21 Released: 2014-02-05
Deposition Author(s): Oksanen, E., Blakeley, M.P., Budayova-Spano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.153 (Depositor), 0.148 (DCC)
R-Value Work:
0.139 (Depositor), 0.134 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation.

Oksanen, E., Blakeley, M.P., El-Hajji, M., Ryde, U., Budayova-Spano, M.

(2014) PLoS One 9: e86651-e86651

PubMed: 24466188 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0086651
Primary Citation Related Structures:
4N3M, 4N9M, 4N9S, 4N9V

PubMed Abstract:
Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10-T57-H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.

Organizational Affiliation

Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives, Grenoble, France, IBS, Centre National de la Recherche Scientifique, Grenoble, France, IBS, Université Grenoble Alpes, Grenoble, France.

Macromolecule Content

Total Structure Weight: 34.92 kDa
Atom Count: 3,054
Modeled Residue Count: 296
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uricase	A	302	Aspergillus flavus	Mutation(s): 1 Gene Names: uaZ, uox EC: 1.7.3.3
UniProt
Find proteins for Q00511 (Aspergillus flavus) Explore Q00511 Go to UniProtKB: Q00511
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00511
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZA Query on AZA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	8-AZAXANTHINE C₄ H₃ N₅ O₂ KVGVQTOQSNJTJI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.153 (Depositor), 0.148 (DCC)
R-Value Work: 0.139 (Depositor), 0.134 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.8	α = 90
b = 95.08	β = 90
c = 104.49	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-02-05

Deposition Author(s):

Oksanen, E.

Blakeley, M.P.

Budayova-Spano, M.

Revision History (Full details and data files)

Version 1.0: 2014-02-05
Type: Initial release
Version 1.1: 2014-02-26
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-06
Changes: Structure summary