Any feedback?
Please rate this page
(all_enzymes.php)
(0/150)

BRENDA support

1.17.4.1: ribonucleoside-diphosphate reductase

This is an abbreviated version!
For detailed information about ribonucleoside-diphosphate reductase, go to the full flat file.

Word Map on EC 1.17.4.1

Reaction

2'-deoxyribonucleoside 5'-diphosphate
+
thioredoxin disulfide
 +
H2O
=
ribonucleoside 5'-diphosphate
 +
thioredoxin

Synonyms

2'-deoxyribonucleoside-diphosphate:oxidized-thioredoxin 2'-oxidoreductase, ADP reductase, CDP reductase, class I ribonucleotide reductase, class I ribonulceotide reductase, class I RNR, class I RR, class Ia ribonucleotide reductase, class Ia RNR, class Ia RR, class Ib ribonucleotide reductase, class Ib RNR, class Ic ribonucleotide reductase, class II RNR, manganese-ribonucleotide reductase, Mn-RNR, More, mRR, NrdA, NrdB, NrdE, NrdF, nucleoside diphosphate reductase, p53-inducible ribonucleotide reductase, R2F, reductase, ribonucleoside diphosphate, ribonucleoside 5'-diphosphate reductase, ribonucleoside diphosphate reductase, ribonucleoside-diphosphate reductase subunit M2 B, ribonucleotide diphosphate reductase, ribonucleotide reductase, RIR1, RIR2, RNR, RNR1 rRibonucleoside-diphosphate reductase large chain 1, RNR2, UDP reductase

ECTree

     1 Oxidoreductases
         1.17 Acting on CH or CH2 groups
             1.17.4 With a disulfide as acceptor
                1.17.4.1 ribonucleoside-diphosphate reductase

Crystallization

Crystallization on EC 1.17.4.1 - ribonucleoside-diphosphate reductase

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method
subunit R2, X-ray diffraction structure determination and analysis at 2.75-2.90 A resolution
-
R2F, sitting drop vapour diffusion method, at 4°C, mixing 0.001 ml of RNR solution, containing mM KCl, 50 mM Tris–HCl, 2 mM DTT, 15% glycerol, pH 7.5, with 0.001 ml of reservoir buffer solution containing 0.1 M sodium citrate, 27.5% PEG 4000, 0.05 M ammonium acetate, pH 6.0, and 0.1 M ammonium acetate pH 7.0 with 0.05 MTris-HCl, pH 7.5, X-ray diffraction structure determination and analysis at 1.36 A resolution
-
B2 subunit, hanging drop method, crystallization in 20% polyethylene glycol 4000, 200 mM NaCl, 0.3% dioxane, 50 mM ethyl mercuric thiosalicylate, 50 mM MES buffer, pH 6.0, orthorhombic crystals, crystal structure at 2.2 A resolution
-
B2 subunit, hanging drops of 0.01 ml containing 25 mg/ml of enzyme with 1 ml of 1.5 M ammonium sulfate in the well and 750 mM ammonium sulfate starting concentration in the drop, pH 6.0, crystals appear after 1 week at room temperatur
-
complex between NrdIox and MnII 2-NrdF, Two NrdI and two NrdF molecules are present in the asymmetric unit, X-ray diffraction structure determination and analysis at 2.5 A resolution
crystals are grown using the hanging drop vapor diffusion technique
free radical subunit R2, basic motif is a bundle of eight long helices. R2 dimer has two equivalent dinuclear iron centers. Iron atoms have both histidine and carboxyl acid ligands and are bridged by the carboxylate group of E115. The essential residue Y122 is buried inside the protein and the tyrosyl radical cannot participate directly in hydrogen abstraction
-
mutant Y122H of R2 protein subunit
structure of a complex between alpha2 and beta2 subunits forming an unprecedented alpha4beta4 ring-like structure in the presence of the negative activity effector dATP, while the active conformation is alpha2beta2. Under physiological conditions, the enzyme exists as a mixture of transient alpha2beta2 and alpha4beta4 species whose distributions are modulated by allosteric effectors. This interconversion between entails dramatic subunit rearrangements
two-dimensional crystals of B1 dimer enzyme-effector complex, 18 A resolution
-
purified recombinant His6-tagged hp53R2, sitting drop vapor diffusion method, at 25°C, 0.002 ml of 4.5 mg/ml protein in 20 mM Tris, pH 7.5, are mixed with 150 mM NaCl and 0.002 ml of precipitant solution containing 0.1 M sodium citrate, pH 6.45, 1.3 M Li2SO4, and 0.5 M (NH4)2SO4, reservoir volume is 0.250 ml, 7-14 days, addition of ferrous ammonium sulfate of 5 mM 1 h prior to harvesting, X-ray diffraction structure determination and analysis at 2.6 A resolution
-
subunit RR1 in complex with TTP, dATP, TTP/GDP, TTP/ATP, and TTP/dATP, 1. TTP bound at the S-site, 2. dATP bound at the S-site, 3. TTP bound at the S-site and GDP at the C-site, 4. TTP bound at the S-site and ATP at the A-site, and 5. TTP bound at the S-site and dATP at the A-site, X-ray diffraction structure determination and analysis at resolutions of 2.4 A, 2.3 A, 3.2 A, 3.1 A, and 3.1 A, respectively
-
small subunit R2 of ribonucleotide reductase, at 4°C and 20°C, 10 mg/ml protein in 20 mM HEPES, pH 7.5, 300 mM NaCl, 10% glycerol, 0.1 mg/ml chymotrypsin, and 0.1 M hexamine cobalt(III) chloride, is mixed with optimized reservoir solution containing 14% w/v PEG 8000, 0.2 M MgCl2,0.1 M Tris-HCl pH 8.2, optimization of the crystallization conditions, X-ray diffraction structure determination and analysis at 2.0 A resolution
-
hanging drop method
alpha subunit, in apo form, in complex with AMP analogue 5'-adenylyl-beta,gamma-imidodiphosphate, with 5'-adenylyl-beta,gamma-imidodiphosphate and CDP, with 5'-adenylyl-beta,gamma-imidodiphosphate and UDP, with dGTP and ADP, TTP and GDP. Binding of specificity effector rearranges loop 2 and moves residue P294 out of the catalytic site, accomodating substrate binding. substrate binding further rearranges loop2. Cross-talk occurs largely through R293 and Q288 of loop 2. Substrate ribose binds with its 3’ hydroxyl closer than its 2’ hydroxyl to residue C218 of the catalytic redox pair
purified enzyme, formed by recombinant subunits R2 and R4, complexed with inhibitor peptide P7 or peptide Fmoc-P6, 20 mg/ml protein in 0.1 M HEPES, pH 7.5, with 20 mM TTP, 5% glycerol, 5mM DTT, 0.1 M KCL, and 25 mm MgCl2, is mixed with a reservoir solution containing 20-25% PEG 3350, 0.2 M NaCl, and 100 mM HEPES, pH 7.5, soaking of crystals for 4 h in reservoir solution with added inhibitor peptide P6 or P7, followed by soaking of crystals in 25% PEG 3350, 0.2 M NaCl, and 100 mM HEPES, pH 7.5, supplemented with 15% glycerol, X-ray diffraction structure determination and analysis at 2.6 and 2.5 A resolution, respectively
structures of mutanr R293A complexed with dGTP and AMPPNP-CDP reveal that ADP is not bound at the catalytic site, and CDP binds farther from the catalytic site compared to wild type
subunit Rnr1 in complex with gemcitabine diphosphate or with a beta subunit Rnr2 or Rnr4 derived peptide. Binding of gemcitabine diphosphate is different from binding of its analogue CDP. Rnr2 and Rnr4 peptides bind differently from each other and block the formation of the enzyme complex
low-resolution crystal structure of an alpha2beta2 complex
-
hanging drop method, crystal structures of the dimeric class II RNR in complex with four cognate allosteric specificity effector-substrate pairs (dTTP-GDP, dGTP-ADP, dATP-CDP or dATP-UDP), as well as structures with only the different effectors (dATP, dTTP or dGTP)