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3.2.2.1: purine nucleosidase

This is an abbreviated version!
For detailed information about purine nucleosidase, go to the full flat file.

Word Map on EC 3.2.2.1

Reaction

a purine nucleoside
+
H2O
=
D-ribose
 +
a purine base

Synonyms

6-oxopurine nucleosidase, CELE_Y43F8C.13, IAG nucleoside hydrolase, IAG-NH, IAG-nucleoside hydrolase, IAGNH, IG-NH, inosine-adenosine-guanosine nucleoside hydrolase, inosine-adenosine-guanosine-preferring nucleoside hydrolase, inosine-guanosine nucleoside hydrolase, inosine-guanosine-specific nucleoside hydrolase, inosine/adenosine/guanosinepreferring NH, IU-nucleoside hydrolase, IunH, N-ribosyl purine ribohydrolase, N-ribosyl-purine ribohydrolase, NSH3, nucleosidase, nucleosidase g, nucleoside hydrolase, PpNRH1, purine beta-ribosidase, purine hydrolase, purine NRH, Purine nucleosidase, purine nucleoside hydrolase, purine nucleoside N-ribohydrolase, purine ribonucleosidase, purine specific nucleoside hydrolase, purine-preferring nucleoside hydrolase, purine-specific hydrolase, purine-specific inosine-adenosine-guanosine nucleoside hydrolase, purine-specific inosineadenosine-guanosine nucleoside hydrolase, purine-specific NH, purine-specific nucleoside hydrolase, purine-specific ribonucleoside hydrolase, ribonucleoside hydrolase, rih1, rih2, RihC, SsIAG-NH, SslAG-NH, SSO2243, Tb927.3.2960, URH1, URH2, ZmNRH3

ECTree

     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.1 purine nucleosidase

Crystallization

Crystallization on EC 3.2.2.1 - purine nucleosidase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging-drop vapour-diffusion method
-
to 1.65 A resolution. Both residues Cys 253 and Cys 42 are appropriately positioned to interact with the purine ring of the substrate
hanging-drop vapour-diffusion method
-
recombinant His-tagged wild-type enzyme, hanging drop avpour diffusion method, 30-35 mg/ml protein is mixed with an equal volume of a precipitant solution containing 0.1 M HEPES, pH 7.5, 100 mM sodium acetate, 10% w/v PEG 4000, and 10% ethylene glycol, X-ray diffraction structure determination and analysis at 3.35 A resolution, molecular replacement
crystal structure is determined at 1.8 A resolution. It is crystallized using the hanging drop vapor diffusion method, mixing 0.001 ml of protein and 0.001 ml of aprecipitant solution consisting of 100 mM Hepes (pH 7.5), 5% PEG 3350, 5 mM CaCl2, 5 mM CdCl2, and 5 mM MgCl2
in silico docking experiments using flavone, 5-hydroxyflavone, 7-hydroxyflavone, chrysin, apigenin, kaempferol, fisetin, and quercetin. All tested flavonoids show high affinities for the enzyme, the lowest free binding energy ranging from -10.23 to -7.14 kcal/mol
purified recombinant detagged enzyme, in complex with iminoribitol-based competitive inhibitors UAMC-00363, immucillin-A and UAMC-00312, X-ray diffraction structure determination and analysis at 1.28-2.18 A resolution
-
hanging drop vapor diffusion method, using 100 mM Bis-Tris (pH 6.5), 200 mM ammonium sulfate, and 22% (w/v) polyethylene glycol monomethyl ether 3350
-
both soaked and co-crystallized with transition-state inhibitor immucillin H
-
hanging drop vapor diffusion method, unliganded structure and 3-deaza-adenosine complex
in complex with immucillin H, hanging drop vapour diffusion method, with 20% polyethylene glycol 4000 and 0.25 M ammonium sulfate in 10 mM potassium acetate, pH 5.0
in complex with inhibitors, hanging drop vapour diffusion method, using 25% (w/v) PEG 3350 in 100 mM Bis-Tris buffer pH 6.5 and 0.2 M MgCl2
molecular mechanics and dynamics simulations. The ribose release process can be divided into ribose dissociation and ribose release steps The ribose dissociation includes cleavage and exchange stages, in which a metastable 6fold intermediate will recover to an 8fold coordination shell of Ca2+ . The estimated barrier for the rate-determining step of the entire reaction is 13.0 kcal/mol, which is comparable to the experimental value of 16.7 kcal/mol. The gating mechanism arising from loop1 and loop2, as well as key residues around the active pocket, plays an important role in manipulating the ribose release
recombinant His-tagged wild-type enzyme, hanging drop avpour diffusion method, 35 mg/ml protein is mixed with an equal volume of reservori solution containing 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, and 20% w/v PEG 2000 monomethyl ether, X-ray diffraction structure determination and analysis at 2.49 A resolution, molecular replacement