1.7.3.3: factor-independent urate hydroxylase

This is an abbreviated version!
For detailed information about factor-independent urate hydroxylase, go to the full flat file.

Word Map on EC 1.7.3.3

Reaction

Urate
+
O2
+
H2O
=
5-hydroxyisourate
+
H2O2

Synonyms

AaUO, AgUOX, ELITEK, Fasturtec, N-35, Nodule specific uricase, Nodulin 35, Nodulin 35 homolog, Non-symbiotic uricase, oxidase, urate, Rasburicase, Uaz, Uox, Urate oxidase, urate oxidoreductase, UriA, uric acid oxidase, uricase, uricase II, Uricoenzyme, Uricozyme

ECTree

     1 Oxidoreductases
         1.7 Acting on other nitrogenous compounds as donors
             1.7.3 With oxygen as acceptor
                1.7.3.3 factor-independent urate hydroxylase

Crystallization

Crystallization on EC 1.7.3.3 - factor-independent urate hydroxylase

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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
crystallizations are performed using the hanging-drop vapour-diffusion method at 19.9°C, structures of crystals soaked with the substrate uric acid, the inhibitor 8-azaxanthin and allantoin are determined at 1.9-2.2 A resolution, 2 homotetramers comprise the asymmetric crystallographic unit, each subunit contains 2 T-fold domains of topology, which are usually found in purine- and pterin-binding enzymes, the uric acid substrate is bound tightly to the enzyme by interactions with Arg180, Leu222 and Gln223 from one subunit and with Thr67 and sp68 of the neighbouring subunit in the tetramer
; Rasburicase
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crystallization of large proteins in the presence of polyethylene glycol
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crystals of about a few tens of micrometres in size, which is nucleated previously in crystallization batch containing 5% PEG 8000, 100 mM NaCl, 8 mg/ml uox-substrate complex and 100 mM Tris-HCl pH 8.5, are used as seeds and their size and quality are further improved using a temperature-control device, large crystals of Uox, co-crystallized with its substrates analogues 8-azaxanthine, 9-methyluric acid or the natural substrate in the presence of cyanide (0.5-2 mg/ml), and soaks with the natural substrate in the absence of cyanide, diffracting to high resolutions are obtained, in the presence of different inhibitors, the crystal form of Uox has a body-centred orthorhombic symmetry and one of the largest primitive unit-cell volumes (a: 80 A, b: 96 A, c: 106 A)
-
enzyme in complex with substrate urate and inhibitor cyanide, X-ray diffraction structure determination and analysis
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hanging drop vapour diffusion method
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ligand-free Uox crystallized with NH4Cl and 15% (w/v) PEG 8000, ligand-free Uox crystallized in water with 10% (w/v) PEG 8000, ligand-free Uox crystallized with NaCl and 15% (w/v) PEG 8000, ligand-free Uox crystallized with (NH4)2SO4 and 15% (w/v) PEG 8000, ligand-free Uox crystallized with NaCl and 8% PEG 8000, ligand-free Uox crystallized with KCl and 10% (w/v) PEG 8000, and Uox complexed with 8-azaxanthine and crystallized with NaCl and 10% (w/v) PEG 8000, in 50 mM Tris buffer pH 8.0
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quantum mechanical/molecular mechanical calculations based on PDB entry 4N9M. The oxidation consists of chemical transformation from 8-hydroxyxythine to an anionic radical via a proton transfer along with an electron transfer, proton transfer to the O2- anion (radical), diradical recombination to form a peroxo intermediate, and dissociation of H2O2 to generate the dehydrourate. Hydration is initiated by the nucleophilic attack of a water molecule on dehydrourate, along with a concerted proton transfer through residue Thr69 in the catalytic site. Hydration is the rate-determining step
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recombinant enzyme in complex with inhibitor 8-azaxanthine in presence of O2 or Cl-, batch technique at room temperature, 10-15 mg/ml protein with an excess of 0.5-2 mg/ml of 8-azaxanthin in 50 mM Tris/HCl, pH 8.5, in the presence of 5-8% w/v PEG 8000 and 0.05 M NaCl, 24-48 h, X-ray diffraction structure determination and analysis at 1.6-1.7 A resolution
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sitting drop vapour diffusion method
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sitting drop vapour diffusion method using buffered D2O
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sitting-drop vapour-diffusion method at room temperature
-
sitting-drop vapour-difusion method. Four different crystal forms of Uox are analyzed. In the presence of uracil and 5,6-diaminouracil crystals usually belong to the trigonal space group P3(1)21, the asymmetric unit of which contains one tetramer of Uox. Chemical oxidation of 5,6-diaminouracil within the protein may occur, leading to the canonical (I222) packing with one subunit per asymmetric unit. Coexistence of two crystal forms, P2(1) with two tetramers per asymmetric unit and I222, is found in the same crystallization drop containing another inhibitor, guanine. A fourth form, P2(1)2(1)2 with one tetramer per asymmetric unit, results in the presence of cymelarsan, an additive
-
structure to 1.4 A resolution, showing a homotetramer containing two homodimers. In each homodimer H-bonds are found between residues E311 and Y249 and between Y319 and D257. Electrostatic interaction networks surround D307 plus R310 and intersubunit R3, K312 plus D257, E318 plus K242, and L322 plus R258
-
homology modeling of monomeric enzyme. The highly conserved residue Gly290 could interact with Asn262 and His264. Residue substitutions near Gly290 may affect its spatial orientation and result in changes in catalysis.Gly290 is likely to participate in the structure of the active site and to be involved in oxygen-binding
to 1.93 A resolution. Space group P212121 with unit cell parameters a 69.16 A, b 139.31 A, c 256.33 A, and alpha =beta =gamma =90°