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2.4.2.1: purine-nucleoside phosphorylase

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

Word Map on EC 2.4.2.1

Reaction

purine 2'-deoxyribonucleoside
+
phosphate
=
purine
 +
2-deoxy-alpha-D-ribose 1-phosphate

Synonyms

5'-deoxy-5'-methylthioadenosine phosphorylase II, 5'-methythioadenosine phosphorylase, adenine nucleoside phosphorylase, adenosine phosphorylase, AgPNP, AmPNP, ANP, ApMTAP, apPNP, bovPNP, bPNO, CKP1, cytokinin riboside phosphorylase, DeoD, deoD_1, DgPNP, EC592_06680, EcPNP, flB, GsPNPI, GsPNPII, GtPNP, hPNP, HpPNP, HsPNO, HsPNP, Ino-Guo phosphorylase, inosine phosphorylase, inosine-guanosine phosphorylase, KlacPNP, KLLA0_C16621g, MTAPII, MtbPNP, nucleotide phosphatase (2.4.2.1), PfPNP, phosphorylase, purine nucleoside, PiPNP, PNP, PNP 1, PNP 2, PNP I, PNP II, PNP-II, PNP-Zg, PNPase, pNPI, PNPII, Pu-NPase, punA, PUNP, PUNPI, PUNPII, purine deoxynucleoside phosphorylase, purine deoxyribonucleoside phosphorylase, purine nucleoside orthophosphate ribosyl transferase, purine nucleoside phosphorylase, purine nucleoside phosphorylase 1, purine nucleoside phosphorylase 2, purine nucleoside phosphorylase DeoD, purine nucleoside phosphorylase DeoD-type, purine nucleoside phosphorylase II, purine ribonucleoside phosphorylase, purine-nucleoside phosphorylases II, SalT, SSO2343, TgPNP, TTC0194, TTC1070, TtPNPI, TtPNPII, TvPNP, xanthosine phosphorylase, XAP, xapA, ylmD

ECTree

     2 Transferases
         2.4 Glycosyltransferases
             2.4.2 Pentosyltransferases
                2.4.2.1 purine-nucleoside phosphorylase

Crystallization

Crystallization on EC 2.4.2.1 - purine-nucleoside phosphorylase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of AgPNP is determined in complex with 5'-deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-H and phosphate to a resolution of 2.2 A
2.24 A resolution
Crystals belonging to space groups P321, P212121, P6322 and H32 are grown in distinct conditions with pH values ranging from 4.2 to 10.5. The crystals diffracts to maximum resolutions ranging from 2.65 to 1.70 A
homology modeling of complexes with ligands guanine, guanosine, 3-deoxyguanosine, 7-methyl-6-thioguanosine, acyclovir and inosine. The structure of the model is stable during molecular dynamics simulation, and does not exhibit loosely structured loop regions or domain terminals
-
binary complex of the trimeric enzyme with the potent ground-state analog inhibitor 9-(5,5-difluoro-5-phosphonopentyl)guanine crystallized in the cubic space group P2(1)3 with unit-cell parameter a = 93.183 A
-
calorimetric titration of recombinant calf PNP complexed with immucillin H. Stoichiometry shows three immucillin molecules per enzyme trimer, enzyme does not show negative cooperativity. One-third-of-the-sites binding does not occur for trimeric enzyme
-
enzyme/inhibitor complex
hanging drop method, purine nucleoside phosphorylase complexed with substrates and substrate analogues
-
high-resolution structure may serve for design of inhibitors with potential pharmacological application
X-ray crystal structure for purine nucleoside phosphorylase with bound 9-deazainosine and inorganic sulfate
-
complex of enzyme with hypoxanthine at 2.15 A resolution, structural data from crystal structure may be useful in designing prodrugs that can be activated by Escherichia coli enzyme but not the human enzyme
-
crystal structures of the wild type in complexes with phosphate and sulfate, respectively, and of the R24A mutant in complex with phosphate/sulfate, to about 2 A resolution. The structural data show that previously observed conformational change is a result of the phosphate binding and its interaction with residue Arg24
crystal structures of the wild-type and a C-terminal KH/S1 domain-truncated mutant of PNPase at resolutions of 2.6 A and 2.8 A, respectively
-
crystals for X-ray analysis are obtained by vapor-diffusion equilibration of droplets hanging from siliconized coverslips inverted on Linbro plates
-
hanging drop method, crystal structure of the ternary complex of the hexameric enzyme with formycin A derivatives and phosphate or sulfate ions is determined at 2.0 A resolution
hanging drop vapor diffusion method. Enzyme in complex with nucleoside analogs: 2-fluoroadenosine, 9-beta-D-ribofuranosyl-6-methylthiopurine, 2-fluoro-2'-deoxyadenosine, 9-beta-D-(2-deoxyribofuranosyl)-6-methylthiopurine, adenosine, formycin B, 7-deazaadenosine, 9-beta-D-arabinofuranosyl-adenine, 9-beta-D-xylofuranosyl-adenine or inosine
purified enzyme PNP in complex with inhibitor ACV, liquid diffusion method, mixing of 0.0035 ml of 32 mg/ml protein in 0.02 M Tris-HCl, pH 7.5, with 0.0035 ml of reservoir solution containing 25% ammonium sulfate, 0.05 M sodium citrate, pH 4.9, 0.04% sodium azide, and 5 mM acycloguanosine, and equilbration against 0.18 ml of reservoir solution, X-ray diffraction structure determination at 2.32 A resolution using the molecular replacement method. The ACV molecule is observed in two conformations and sulfate ions are located in both the nucleoside-binding and phosphate-binding pockets of the enzyme
purified recombinant enzyme, crystals are grown in microgravity by the capillary counterdiffusion method through a gel layer, X-ray diffraction structure determination and analysis at 0.99 A resolution, molecular replacement using the structure of the hexameric Escherichia coli enzyme, PDB ID 1ECP, as template
ternary complex of enzyme with a phosphate ion and formycin A, to 0.975 A resolution. The structure reveals, in some active sites, an unexpected binding site for phosphate and exhibits a stoichiometry of two phosphate molecules per enzyme subunit. In these active sites, the phosphate and nucleoside molecules are found not to be in direct contact but being bridged by three water molecules
two crystal forms in presence of guanine and phosphate and a third crystal form in presence of xanthine and phosphate, crystals are grown at pH values between 8 and 9, crystals can not be grown at physiologic pH, no good crystals can be obtained in presence of xanthosine, guanosine or ribose 1-phosphate
to 2.4 A resolution, space group R3. alpha/beta structure with a nine-stranded mixed beta-barrel flanked by a total of nine alpha-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively
-
purified recombinant enzyme in apoform and in complex with phosphate and with formycin A as binary and ternary complexes, X-ray diffraction structure determination and analysis
purified recombinant enzyme PNP-Zg in ternary complex with hypoxanthine and phosphate molecules, obtained from three different crystallization conditions: B8 (0.2 M MgCl2, 0.1 M Tris-HCl, pH 7.0, 10 % PEG 8000 for structure HpPNP-1), A1 (0.2 M Li2SO4, 0.1 M Na acetate, pH 4.5, 50 % PEG 400 for structure HpPNP-2) and D3 (0.2 M Na chloride, 0.1 M Na/K phosphate, pH 6.2, 50% PEG 200 for structure HpPNP-3), 20°C, X-ray diffraction structure determination and analysis at 2.3-2.4 A resolution, molecular replacement using the structure of Escherichia coli PNP (PDB ID 1K9S) as template
cocrystallization of L-immucillin-H and 4'-deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-H with the enzyme and phosphate. The structures with L-immucillin-H and 4'-deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-H are solved to 2.9 A and 2.1 A resolution, respectively
conformational states in complex with transition state analogues Immucillin-H and DATMe-Immucillin-H. The (purine nucelotide phosphorylase)3(PO4)3 ImmH-complex is more compact by sedimentation rate than the other complexes. Purine nucelotide phosphorylase protein conformation of dynamic motion correlates more closely with entropy of binding than with affinity. Catalytically active turnover with saturated substrate sites causes less change in peptide amide deuterium exchange and sedimentation rates than binding of transition state analogues. DATMe-Immucilin-H more closely mimics the transition of human PNP than does Immucilin-H and achieves strong binding interactions at the catalytic site while causing relatively modest alterations of the protein dynamic motion
crystals for X-ray analysis are obtained by vapor-diffusion equilibration of droplets hanging from siliconized coverslips inverted on Linbro plates
-
hanging drop vapour diffusion. Crystallographic structure of human PNP in complex with guanosine (at 2.80 A resolution), 3'-deoxyguanosine (at 2.86 A resolution) and 8-azaguanine (at 2.85 A resolution)
HsPNP/4'-deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-H/SO4 crystal complexes are prepared by hanging-drop vapor diffusion, HsPNP/immucillin-H/PO4 crystal complexes are prepared by sitting-drop vapor diffusion
in complex with 2-mercapto-4(3H)-quinazolinone at 2.7 A resolution, application to predict ligand positions obtained in docking simulations
in complex with 7-deazaguanine, to 2.75 A resolution. Two intermolecular hydrogen bonds involve the residues Glu201 and Asn243
in complex with transition-state analogues immucillin-H, DADMe-immucillin-H, DATMe-immucillin-H, and immucillin-H, to 2.4 A to 2.5 A resolution. Inhibitor binding sites of purine nucelotide phosphorylase are near the C-terminal region of the 6-stranded beta-sheet. The purine base binding region consists primarily of hydrophobic residues including Phe200, Val217, Met219, Val245, and Val260. Purine base interactions also include the polar residues Glu201 and Asn243 as hydrogen bond acceptors from the NH1 and NH7 groups of 9-deazahypoxanthine. Asn243 also donates hydrogen bonds to O6 of the deazapurine, except in the case of immucillin-H. Features of tight binding are ion-pair formation between bound phosphate or its mimic and inhibitor cation, leaving-group interactions to N1, O6, and N7 of 9-deazahypoxanthine, interaction between phosphate and inhibitor hydroxyl groups, and His257 interacting with the 5'-hydroxyl group
mutant E201Q/N243D in complex with prodrug 2-fluoro-2'-deoxyadenosine and with 2-fluoroadenine. The overall fold of the mutant is nearly identical to the wild type enzyme. The residues Gln201 and Asp243 introduced by the mutation form hydrogen bond contacts with 2-fluoro-2'-deoxyadenosine that result in its binding and catalysis. Comparison of complexes suggest that the side chains of Gln201 and Asp243 as well as the purine base rotate during catalysis possibly facilitating cleavage of the glycosidic bond
recombinant enzyme in complex with 7-methyl-6-thio-guanosine
-
purified enzyme KlacPNP in complex with hypoxanthine, screening of recombinant N- and C-terminally His6-tagged wild-type enzyme, vapor diffusion sitting drop, mixing of 0.00125 ml of 8 mg/ml of protein in 25 mM Tris-HCl, 100 mM NaCl, pH 8.0, with 0.00125 ml of mother liquor consisting of 0.1 M sodium acetate trihydrate, pH 4.6, and 8% PEG 4000, X-ray diffraction structure determination and analysis at 1.97 A resolution, molecular replacement using the human PNP as a search template (PDB ID 3PHB)
modeling of complexes with ligands acyclovir, guanine, 7-methyl-6-thioguanosine, 3-deoxyguanosine, guanosine and inosine and comparative analysis of models with human and Liseria monocytogenes enzymes
-
analysis of the structures of MTI (PDB ID 1Q1G) and DADMe-I (PDB ID 3PHC) co-crystallized with the protein structure of PfPNP
enzyme in complex with the inhibitor 5'-methylthio-immucillin-H, hanging-drop vapor-diffusion method
-
in complex with phosphate and immucillin-H, sitting drop vapor diffusion method, using 25% (w/v) polyethylene glycol monomethyl ether 2000, 100 mM Tris (pH 8.5), and 0.2 M trimethylamine N-oxide dihydrate
-
modeling of the inhibitors 1-((2-pyrrolidine-1-yl)ethyl)uracil and 3-((2-pyrrolidine-1-yl)ethyl)uracil into the active site of the protein, PDB entry 1NW4, by superposition of the uracil ring and the purine ring of Immucillin-H. Both compounds can fit adequately in the active site. In both cases the uracil base is predicted to be oriented in the nucleoside binding pocket by a pi-stacking similar to the purine base of Immucillin-H. The N1 of the uracil base in 1-((2-pyrrolidine-1-yl)ethyl)uracil and the N3 of the uracil base in 3-((2-pyrrolidine-1-yl)ethyl)uracil roughly superimpose with the C4 of Immucillin-H
molecular dynamics simulation in ligand free form and in complex with immucillin and sulfate. The overall structures are stable along the molecular dynamics simulations
-
mutant Y160F/V66I/V73I in complex with immucillin H, sitting drop vapor diffusion method, using 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES at pH 7.5, and 30% (v/v) 2-propanol
structures of purine nucleoside phosphorylase complexed with sulfate and its natural substrate inosine
-
construction of three-dimensional model
hanging-drop vapor-diffusion method, 1. enzyme in complex with sulfobetaine 195 and acetate, 2. enzyme in complex with both phosphate and acetate, 3. enzyme in complex with acetate
-
in complex with adenine, adenosine, inosine, and hypoxanthine to 1.4 A resolution
in complex with inhibitor 6-amino-5-bromopyrimidine-2,4(1H,3H)-dione, to 1.9 A resolution
to 1.6 A resolution, space group H3
-
structural model of enzyme in complex with ligands guanine, guanosine, 3-deoxyguanosine, 7-methyl-6-thio-guanosine, acyclovir, and inosine. Molecular dynamics simulation and comparison with human enzyme
-
crystallizes in space group P4(3)2(1)2 with the unit cell dimensions a = 131.9 A, c = 169.9 A, 1.9 A resolution
-
in complex with phosphate and immucillin-H, sitting drop vapor diffusion method, using 25% (w/v) polyethylene glycol monomethyl ether 2000, 100 mM Tris (pH 8.5), and 0.2 M trimethylamine N-oxide dihydrate
crystal structures of the TvPNP/immucillin-A/PO4 and TvPNP/4'-deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-A/PO4 ternary complexes
-
crystal structures of the TvPNP/immucillin-A/PO4 and TvPNP/deaza-1'-aza-2'-deoxy-1'-(9-methylene)-immucillin-A /PO4 ternary complexes.
-
structures of the enzyme complexed with 2-fluoro-2'-deoxyadenosine, formycin A, adenosine, inosine or 2'-deoxyinosine determined at resolutions ranging from 2.4 to 2.9 A
-