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
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1.17.4.1
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deoxyribonucleotides
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hydroxyurea
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tyrosyl
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reductases
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chlamydia
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trachomatis
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deoxynucleotides
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proton-coupled
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diiron
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deoxycytidine
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diferric
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thiyl
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dntps
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dcdp
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thiosemicarbazone
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diferric-tyrosyl
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nrdabs
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hydroxyurea-resistant
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medicine
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nrdef
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heterodinuclear
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drug development
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antiferromagnetically
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pharmacology
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molecular biology
- 1.17.4.1
- deoxyribonucleotides
- hydroxyurea
-
tyrosyl
- reductases
- chlamydia
- trachomatis
-
deoxynucleotides
-
proton-coupled
-
diiron
- deoxycytidine
-
diferric
-
thiyl
- dntps
- dcdp
- thiosemicarbazone
-
diferric-tyrosyl
-
nrdabs
-
hydroxyurea-resistant
- medicine
-
nrdef
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heterodinuclear
- drug development
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antiferromagnetically
- pharmacology
- molecular biology
Reaction
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
1.17.4.1 ribonucleoside-diphosphate reductaseAdvanced search results
results (
results (Subunits
Subunits on EC 1.17.4.1 - ribonucleoside-diphosphate reductase
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SUBUNIT 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dimer
heterodimer
eukaryotic RNRs comprise alpha2beta2 heterodimers, the large and small subunits show strong interaction
monomer
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beta-subunit is predominantly a dimer, whereas the alpha-subunit is in a nucleotide-dependent equilibrium between monomers, dimers, and tetramers. The alpha2beta2 complex is the major active form
monomer or dimer
multimer
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alphanbetan multi-subunit protein complex consisting of subunit types RR1 and RR2, the alpha or RR1 subunit contains the catalytic C site and two allosteric sites, while the beta or RR2 subunit houses a stable tyrosyl free radical that is transferred some 35 A to the catalytic site to initiate radical-based chemistry on the substrate
octamer
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4 * 107000, subunit NrdA + 4 * 47000, subunit NrdB, SDS-PAGE
oligomer
tetramer
trimer
alpha,beta2, 1 * 81200 + 2 * 37900, deduced from nucleotide sequence
additional information
?
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x * 84000 + x * 58000, 84000 Da subunit is predominantly monomeric under experimental conditions, 58000 Da subunit may be oligomeric, SDS-PAGE
?
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x * 45000 + 1 * 75000 + 1 * 45000, holoenzyme may have an alpha4,beta,beta' structure, SDS-PAGE
?
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2 * 90000 + x * 75000, most likely 1 75000 Da subunit, SDS-PAGE
dimer
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alphabeta, class Ib RNR is composed of two subunits alpha (NrdE) and beta (NrdF). Beta contains the metallo-cofactor, essential for the initiation of the reduction process
dimer
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alphabeta, class Ib RNR is composed of two subunits alpha (NrdE) and beta (NrdF). Beta contains the metallo-cofactor, essential for the initiation of the reduction process
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dimer
Herpes simplex virus
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1 * 136000 + 1 * 38000, molecular weight for subunit 1 deduced from sequence: 124017 Da, difference may be due to phosphorylation, SDS-PAGE
dimer
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2 * 60200, dimer appears to dissociate in the absence of Ca2+ into monomers, SDS-PAGE
dimer
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beta-subunit is predominantly a dimer, whereas the alpha-subunit is in a nucleotide-dependent equilibrium between monomers, dimers, and tetramers. The alpha2beta2 complex is the major active form
monomer or dimer
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class II enzymes show a monomeric or dimeric structure
monomer or dimer
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class II enzymes show a monomeric or dimeric structure
oligomer
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RNRs are composed of alpha- and beta-subunits that form active (alpha)n(beta)m, with n or m being 2 or 6, complexes. Subunit alpha binds NDP substrates, i.e. CDP, UDP, ADP, and GDP, C site, as well as ATP and dNTPs, i.e. dATP, dGTP, TTP, allosteric effectors that control enzyme activity (A site) and substrate specificity, S site
oligomer
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class I enzyme show a alpha2beta2 complex structure, modeling
oligomer
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class I enzyme show a alpha2beta2 complex structure, modeling
tetramer
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alpha2,beta2, 160000 Da subunit B1 and 78000 Da subunit B2, each consisting of 2 identical or similar proteins
tetramer
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alpha,alpha'beta2, 2 * 82000 + 2 * 78000, each subunit composed of 2 polypeptide chains, subunit B1, 82000 Da, sedimentation equilibrium centrifugation, subunit B2, low speed sedimentation equilibrium centrifugation
tetramer
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class I RNR is a tetramer formed by two homodimers, subunit R1 encoded by the nrdA gene and subunit R2 encoded by the nrdB gene
tetramer
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class Ib RNR is composed of two homodimeric subunits: alpha2 or NrdE, where nucleotide reduction occurs, and beta2 or NrdF, which contains an unidentified metallocofactor that initiates nucleotide reduction
tetramer
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class I RNR is a tetramer formed by two homodimers, subunit R1 encoded by the nrdA gene and subunit R2 encoded by the nrdB gene
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tetramer
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alpha2,beta2, 160000 Da subunit B1 and 78000 Da subunit B2, each consisting of 2 identical or similar proteins
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tetramer
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2 * 160000, subunit R1, + 2 * 78000, subunit R2, the catalytic active enzyme forms a dimer of homodimers
tetramer
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RNR is a tetramer consisting of two non-identical homodimers. The two identical M2 subunits regulate the substrate specificity of the enzyme, while the other two identical M1 subunits are responsible for the activity by binding the ribonucleotides and allosteric effectors
tetramer
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the enzyme consists of M1, M2, and p53R2 subunits in an alphabeta2gamma constellation
tetramer
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4 * 37 442.98, subunit R2, mass spectrometry, 4 * 31000, recombinant subunit R2, SDS-PAGE
tetramer
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alpha2,betabeta, 2 * 96900 (PFR1) + 1 * 40600 (PFR2) + 1 * 39000 (PFR4), SDS-PAGE
tetramer
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beta-subunit is predominantly a dimer, whereas the alpha-subunit is in a nucleotide-dependent equilibrium between monomers, dimers, and tetramers. The alpha2beta2 complex is the major active form
tetramer
the enzyme activity requires formation of a complex between subunits R1 and R2 in which the R2 C-terminal peptide binds to R1
tetramer
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alpha2,beta2, 2 * 70000 + 2 * 36000, SDS-PAGE
tetramer
Tequatrovirus T4
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alpha2beta2, 2 * 85000 + 2 * 35000, enzyme induced in Escherichia coli after infection with bacteriophage T4, SDS-PAGE
additional information
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at physiological concentrations, alpha-subunit NrdE is a monomer and beta-subunit NrdF in complex with dimanganic-tyrosyl radical cofactor is a dimer. A 1:1 mixture of NrdE:NrdF, however, is composed of a complex mixture of structures
additional information
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at physiological concentrations, alpha-subunit NrdE is a monomer and beta-subunit NrdF in complex with dimanganic-tyrosyl radical cofactor is a dimer. A 1:1 mixture of NrdE:NrdF, however, is composed of a complex mixture of structures
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additional information
interaction of the alpha2 and beta2 subunits during the reaction, comparison to the RNR from Escherichia coli, overview
additional information
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interaction of the alpha2 and beta2 subunits during the reaction, comparison to the RNR from Escherichia coli, overview
additional information
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hybrid holoenzyme, consisting of the small manganese-containing R2F subunit and the large catalytic subunit R1E
additional information
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hybrid holoenzyme, consisting of the small manganese-containing R2F subunit and the large catalytic subunit R1E
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additional information
proposed in vitro mechanism for the assembly of the diferric tyrosyl radical cofactor of subunit R2
additional information
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the active form of B2 subunit contains a tyrosyl radical essential for activity
additional information
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the active form of B2 subunit contains a tyrosyl radical essential for activity
additional information
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each catalytic turnover by aerobic ribonucleotide reductase requires the assembly of the two proteins, R1 (alpha2) and R2 (beta2), to produce deoxyribonucleotides for DNA synthesis
additional information
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2 * R1 subunit + 2 * R2 subunit, cross-talk Between the C-terminus of one subunit R1 monomer and the active site of its neighboring monomer, overview
additional information
interaction of the alpha2 and beta2 subunits during the reaction, comparison to the RNR from Chlamydia trachomatis, overview
additional information
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structure comparisons of classI-III RNRs, model for the subunit organization of RNRs, overview
additional information
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structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview
additional information
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subunit R1 contains the substrate binding site and catalyzes dehydroxylation of the 2'-hydroxyl group of the ribose ring. The tyrosine radical in R2 is in the neutral deprotonated form with the oxidized Fe(III)Fe(III) active site
additional information
a complex between alpha2 and beta2 subunits forms 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
additional information
ribonucleoside-diphosphate reductase subunit M2 B may substitute for small enzyme subunit hRRM2 to form a functional holoenzyme with large subunit hRRM1. The holoenzyme with subunit M2 B can only achieve 40-75% kinetic activity of that with hRRM2. Both small subunits share the same binding site on large subunit hRRM1. The effectors ATP or dATP can regulate holoenzyme activity independent of the small subunit
additional information
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one monomer can swivel between two conformations and impose significant influences on helix D and helix B of the opposite monomer. This change ultimately affects the orientation of D100 and, thus, the integrity of the binuclear iron environment. Structural basis of B helix disorder and the N-terminal swivel region, overview
additional information
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dATP-induced oligomerization, overview, modeling of the holo-complex
additional information
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structure comparisons of classI-III RNRs, model for the subunit organization of RNRs, overview
additional information
in hypoxic conditions the small subunit of the ribonucleotide reductase enzyme is switched from RRM2 to RRM2B in order to facilitate nucleotide production and ongoing replication. Specific residues within RRM2B are identified that are responsible for maintaining activity in hypoxia
additional information
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class I RNRs are composed of a heterotetramer, which is in turn composed of two homodimers of the R1 and R2 subunits. The R1 subunit contains the active site as well as the sites for allosteric regulation
additional information
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structure comparisons of classI-III RNRs, model for the subunit organization of RNRs, overview
additional information
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nucleotide binding to the specificity site drives formation of an active R1,2R2,2 dimer, ATP or dATP binding to the adenine-specific site results in formation of an inactive tetramer and ATP binding to the hexamerization site drives formation of an active R1,6R2,6 hexamer which is probably the major active form in mammalian cells
additional information
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enzyme in Ehrlich ascites tumor cells consits of two nonidentical subunits: an effector-binding subunit, EB, and a non-heme iron containing subunit, NHI, since their relative levels are not coordinately regulated the stoichiometry of the whole enzyme varies with the cell cycle
additional information
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composition of the enzyme is not constant, but is altered in presence of effectors
additional information
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large subunit R1 contains binding sites for substrates and allosteric effectors, smaller subunit R2 contains non-heme iron and a tyrosyl free-radical
additional information
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large subunit R1 contains binding sites for substrates and allosteric effectors, smaller subunit R2 contains non-heme iron and a tyrosyl free-radical
additional information
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in presence of dTTP, subunit R1 forms dimers. In presence of dATP or ATP, subunit R1 forms hexamers of 544000 Da, which interact with the subunit R2 dimer to form an enzymatically active protein complex alpha6beta2. The complex can be in activated or inhibited state depending on whether ATP or dATP is bound. Complex alpha6beta2 is the major form of enzyme at physiological levels of subunits and nucleotides
additional information
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structure comparisons of classI-III RNRs, model for the subunit organization of RNRs, overview
additional information
the active class Ib ribonucleotide reductase can use two different small, cofactor-housing subunits, R2F-1 and R2F-2, with similar activity
additional information
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enzyme is a complex of the NrdA protein harboring the active site and the allosteric sites and the NrdB protein harboring a tyrosyl radical. Wild-type enzyme consists of four NrdA and four NrdB subunits. A truncated NrdA lacking the N-terminal ATP-cone forms an NrdA2NrdB2 complex
additional information
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structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview
additional information
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88000-90000 Da M1 subunits are degraded into 40000 Da fragments in proliferately quiescent liver cells, intact subunits are only accumulated when the cells replicate DNA
additional information
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subunits Y1 and Y2 constitute the active enzyme, large subunit Y3 has no activity, subunit Y4 may function as a chaperone
additional information
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C-terminal domain of subunit R1 acts in trans to reduce the active site of its neighbouring monomer and interacts with the N-terminal domain of neighbouring R1. Inhibitor protein Sml1 competes with the C-terminal domain of R1 for association with the N-terminal domain to hinder the accessibility of the CX2C motif to the active site for R1 regeneration during the catalytic cycle
additional information
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enzyme consists of two homodimeric subunits, R1 and R2. In Saccharomyces cerevisiae, there are two R2 subunits named beta and beta, the active form in the holoenzyme being a dimer betabeta. Isoform beta plays a crucial role in cluster assembly
additional information
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under normal conditions, the cell assembles stoichiometric amounts of tyrosyl radicals per betabeta subunit dimer and modulation of tyrosyl radical concentration is not involved in regulation of enzyme activity
additional information
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structure comparisons of classI-III RNRs, model for the subunit organization of RNRs, overview
additional information
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structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview
additional information
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catalytic subunit U2 contains a tyrosyl radical essential for activity
