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Information on EC 1.17.4.1 - ribonucleoside-diphosphate reductase and Organism(s) Corynebacterium ammoniagenes and UniProt Accession O69273

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IUBMB Comments
This enzyme is responsible for the de novo conversion of ribonucleoside diphosphates into deoxyribonucleoside diphosphates, which are essential for DNA synthesis and repair. There are three types of this enzyme differing in their cofactors. Class Ia enzymes contain a diiron(III)-tyrosyl radical, class Ib enzymes contain a dimanganese-tyrosyl radical, and class II enzymes contain adenosylcobalamin. In all cases the cofactors are involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl (alpha-oxoalkyl) radical. The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues. A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position. The disulfide bridge is reduced by the action of thioredoxin. cf. EC 1.1.98.6, ribonucleoside-triphosphate reductase (formate) and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
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Corynebacterium ammoniagenes
UNIPROT: O69273
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The taxonomic range for the selected organisms is: Corynebacterium ammoniagenes
The enzyme appears in selected viruses and cellular organisms
Synonyms
ribonucleoside diphosphate reductase, cdp reductase, class i rnr, class i ribonucleotide reductase, class ia rnr, ribonucleoside-diphosphate reductase, class ia ribonucleotide reductase, adp reductase, p53-inducible ribonucleotide reductase, class ic ribonucleotide reductase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
2'-deoxyribonucleoside-diphosphate:oxidized-thioredoxin 2'-oxidoreductase
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ADP reductase
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CDP reductase
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nucleoside diphosphate reductase
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reductase, ribonucleoside diphosphate
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ribonucleoside 5'-diphosphate reductase
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ribonucleoside diphosphate reductase
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ribonucleotide diphosphate reductase
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ribonucleotide reductase
UDP reductase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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oxidation
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reduction
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SYSTEMATIC NAME
IUBMB Comments
2'-deoxyribonucleoside-5'-diphosphate:thioredoxin-disulfide 2'-oxidoreductase
This enzyme is responsible for the de novo conversion of ribonucleoside diphosphates into deoxyribonucleoside diphosphates, which are essential for DNA synthesis and repair. There are three types of this enzyme differing in their cofactors. Class Ia enzymes contain a diiron(III)-tyrosyl radical, class Ib enzymes contain a dimanganese-tyrosyl radical, and class II enzymes contain adenosylcobalamin. In all cases the cofactors are involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl (alpha-oxoalkyl) radical. The ketyl radical is reduced to 3'-keto-deoxynucleotide concomitant with formation of a disulfide anion radical between two cysteine residues. A proton-coupled electron-transfer from the disulfide radical to the substrate generates a 3'-deoxynucleotide radical, and the final product is formed when the hydrogen atom that was initially removed from the 3'-position of the nucleotide by the thiyl radical is returned to the same position. The disulfide bridge is reduced by the action of thioredoxin. cf. EC 1.1.98.6, ribonucleoside-triphosphate reductase (formate) and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
CAS REGISTRY NUMBER
COMMENTARY hide
9047-64-7
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ribonucleoside diphosphate + reduced thioredoxin
2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O
show the reaction diagram
NrdH-redoxin obtained from an overproducing strain, no activity with E. coli thioredoxin
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ir
additional information
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ribonucleotide reduction is the unique step in DNA-precursor biosynthesis and involves radical-dependent redox chemistry and diverse metallo-cofactors, overview. The Mn-RNR from the Gram-positive bacterium Corynebacterium ammoniagenes, strain ATCC 6872, belongs a distinct RNR class IV enzyme
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
additional information
?
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ribonucleotide reduction is the unique step in DNA-precursor biosynthesis and involves radical-dependent redox chemistry and diverse metallo-cofactors, overview. The Mn-RNR from the Gram-positive bacterium Corynebacterium ammoniagenes, strain ATCC 6872, belongs a distinct RNR class IV enzyme
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
EPR-silent Mn bound to the polypeptide chain, approx. 0.5 mol manganese ions/mol of R2F polypeptide
Mn2+
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R2F is a mangagnese-containing enzyme
additional information
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R2F does not contain the metals Fe, Co, Ni and Cu
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Hydroxyurea
2 mM, approx. 80% inactivation
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ATP
stimulation of CDP reduction
dATP
stimulation of CDP reduction
dTTP
stimulation of CDP reduction
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
class Ib reductase
UniProt
Manually annotated by BRENDA team
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
O69273_CORAM
720
0
81282
TrEMBL
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37900
alpha,beta2, 1 * 81200 + 2 * 37900, deduced from nucleotide sequence
81200
alpha,beta2, 1 * 81200 + 2 * 37900, deduced from nucleotide sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
trimer
alpha,beta2, 1 * 81200 + 2 * 37900, deduced from nucleotide sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
low-salt precipitation, DEAE-cellulose, Supredex 200, Mono Q
recombinant R2F by anion exchange chromatography, gel filtration, and another different step of anion exchange chromatography to homogeneity
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression R1E and R2F subunits in Escherichia coli
recombinant expression of R2F using expression vector pOCA2
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Fieschi, F.; Torrents, E.; Toulokhonova, L.; Jordan, A.; Hellman, U.; Barbe, J.; Gibert, I.; Karlsson, M.; Sjoberg, B.M.
The manganese-containing ribonucleotide reductase of Corynebacterium ammoniagenes is a class Ib enzyme
J. Biol. Chem.
273
4329-4337
1998
Corynebacterium ammoniagenes (O69273)
Manually annotated by BRENDA team
Ogata, H.; Stolle, P.; Stehr, M.; Auling, G.; Lubitz, W.
Crystallization and preliminary X-ray analysis of the small subunit (R2F) of native ribonucleotide reductase from Corynebacterium ammoniagenes
Acta Crystallogr. Sect. F
65
878-880
2009
Corynebacterium ammoniagenes
Manually annotated by BRENDA team