PDBsum entry 7cuc

Oxidoreductase

PDB id: 7cuc

Contents

Protein chains

301 a.a.

Ligands

AZA ×2

OXY ×2

MXE ×6

SO4

Metals

_NA ×2

Waters ×697

PDB id:

7cuc

Name:

Oxidoreductase

Title:

Crystal structure of urate oxidase from bacillus sp. Tb-90 in the absence from chloride anion at 1.44 a resolution

Structure:

Uric acid degradation bifunctional protein. Chain: a, b. Synonym: urate oxidase. Engineered: yes

Source:

Bacillus sp. (Strain tb-90). Organism_taxid: 36824. Strain: tb-90. Gene: uao. Expressed in: escherichia coli dh5[alpha]. Expression_system_taxid: 668369

Resolution:

1.44Å R-factor: 0.177 R-free: 0.208

Authors:

T.Hibi,T.Itoh

Key ref:

T.Hibi and T.Itoh (2021). Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity. J Biochem, 169, 15-23. PubMed id: 33002140 DOI: 10.1093/jb/mvaa114

Date:

22-Aug-20 Release date: 25-Nov-20

Protein chains

Q45697  (PUCL_BACSB) -  Uric acid degradation bifunctional protein from Bacillus sp. (strain TB-90)

Seq: 502 a.a.

Struc: 301 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.7.3.3 - factor independent urate hydroxylase.
• Pathway: AMP Catabolism
• Reaction: urate + O2 + H2O = 5-hydroxyisourate + H2O2

urate + O2 (Bound ligand (Het Group name = OXY) corresponds exactly) + H2O (Bound ligand (Het Group name = AZA) matches with 76.92% similarity) = 5-hydroxyisourate + H2O2

• Cofactor: Copper
• Enzyme class 2: E.C.4.1.1.97 - 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase.
• Reaction: 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate + H⁺ = (S)-allantoin + CO2

5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (Bound ligand (Het Group name = AZA) matches with 66.67% similarity) + H(+) = (S)-allantoin + CO2

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1093/jb/mvaa114

J Biochem 169:15-23 (2021)

PubMed id: 33002140

Identification of quasi-stable water molecules near the Thr73-Lys13 catalytic diad of Bacillus sp. TB-90 urate oxidase by X-ray crystallography with controlled humidity.

T.Hibi, T.Itoh.

ABSTRACT

Urate oxidases (UOs) catalyze the cofactor-independent oxidation of uric acid, and an extensive water network in the active site has been suggested to play an essential role in the catalysis. For our present analysis of the structure and function of the water network, the crystal qualities of Bacillus sp. TB-90 urate oxidase were improved by controlled dehydration using the humid air and glue-coating method. After the dehydration, the P21212 crystals were transformed into the I222 space group, leading to an extension of the maximum resolution to 1.42 Å. The dehydration of the crystals revealed a significant change in the five-water-molecules' binding mode in the vicinity of the catalytic diad, indicating that these molecules are quasi-stable. The pH profile analysis of log(kcat) gave two pKa values: pKa1 at 6.07 ± 0.07 and pKa2 at 7.98 ± 0.13. The site-directed mutagenesis of K13, T73 and N276 involved in the formation of the active-site water network revealed that the activities of these mutant variants were significantly reduced. These structural and kinetic data suggest that the five quasi-stable water molecules play an essential role in the catalysis of the cofactor-independent urate oxidation by reducing the energy penalty for the substrate-binding or an on-off switching for the proton-relay rectification.