8OFK

Crystal structure of the cysteine-rich Gallus gallus urate oxidase in complex with the 8-azaxanthine inhibitor under reducing conditions (space group C 2 2 21)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Cysteine Enrichment Mediates Co-Option of Uricase in Reptilian Skin and Transition to Uricotelism.

Mori, G.Liuzzi, A.Ronda, L.Di Palma, M.Chegkazi, M.S.Bui, S.Garcia-Maya, M.Ragazzini, J.Malatesta, M.Della Monica, E.Rivetti, C.Antin, P.B.Bettati, S.Steiner, R.A.Percudani, R.

(2023) Mol Biol Evol 40

  • DOI: https://doi.org/10.1093/molbev/msad200
  • Primary Citation of Related Structures:  
    8OFK, 8OH8, 8OIH, 8OIW

  • PubMed Abstract: 

    Uric acid is the main means of nitrogen excretion in uricotelic vertebrates (birds and reptiles) and the end product of purine catabolism in humans and a few other mammals. While uricase is inactivated in mammals unable to degrade urate, the presence of orthologous genes without inactivating mutations in avian and reptilian genomes is unexplained. Here we show that the Gallus gallus gene we name cysteine-rich urate oxidase (CRUOX) encodes a functional protein representing a unique case of cysteine enrichment in the evolution of vertebrate orthologous genes. CRUOX retains the ability to catalyze urate oxidation to hydrogen peroxide and 5-hydroxyisourate (HIU), albeit with a 100-fold reduced efficiency. However, differently from all uricases hitherto characterized, it can also facilitate urate regeneration from HIU, a catalytic property that we propose depends on its enrichment in cysteine residues. X-ray structural analysis highlights differences in the active site compared to known orthologs and suggests a mechanism for cysteine-mediated self-aggregation under H2O2-oxidative conditions. Cysteine enrichment was concurrent with the transition to uricotelism and a shift in gene expression from the liver to the skin where CRUOX is co-expressed with β-keratins. Therefore, the loss of urate degradation in amniotes has followed opposite evolutionary trajectories: while uricase has been eliminated by pseudogenization in some mammals, it has been repurposed as a redox-sensitive enzyme in the reptilian skin.


  • Organizational Affiliation

    Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UricaseA [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
343Gallus gallusMutation(s): 0 
Gene Names: LOC101747367
EC: 1.7.3.3
UniProt
Find proteins for A0A8V0ZED1 (Gallus gallus)
Explore A0A8V0ZED1 
Go to UniProtKB:  A0A8V0ZED1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8V0ZED1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AZA (Subject of Investigation/LOI)
Query on AZA

Download Ideal Coordinates CCD File 
DA [auth CCC],
E [auth AAA],
MA [auth DDD],
R [auth BBB]
8-AZAXANTHINE
C4 H3 N5 O2
KVGVQTOQSNJTJI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth CCC]
G [auth AAA]
GA [auth CCC]
H [auth AAA]
HA [auth CCC]
FA [auth CCC],
G [auth AAA],
GA [auth CCC],
H [auth AAA],
HA [auth CCC],
I [auth AAA],
IA [auth CCC],
J [auth AAA],
JA [auth CCC],
K [auth AAA],
KA [auth CCC],
L [auth AAA],
M [auth AAA],
OA [auth DDD],
PA [auth DDD],
QA [auth DDD],
RA [auth DDD],
S [auth BBB],
SA [auth DDD],
T [auth BBB],
TA [auth DDD],
U [auth BBB],
UA [auth DDD],
V [auth BBB],
VA [auth DDD],
W [auth BBB],
X [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth BBB]
BA [auth BBB]
CA [auth BBB]
LA [auth CCC]
N [auth AAA]
AA [auth BBB],
BA [auth BBB],
CA [auth BBB],
LA [auth CCC],
N [auth AAA],
O [auth AAA],
P [auth AAA],
WA [auth DDD],
XA [auth DDD],
Y [auth BBB],
YA [auth DDD],
Z [auth BBB]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
EA [auth CCC],
F [auth AAA],
NA [auth DDD],
Q [auth BBB]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.195α = 90
b = 125.475β = 90
c = 238.581γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/P000169/1
Italian Ministry of EducationItaly2017483NH8

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release