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Information on EC 1.1.98.6 - ribonucleoside-triphosphate reductase (formate)
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1.1.98.6 ribonucleoside-triphosphate reductase (formate)IUBMB Comments
The enzyme, which is expressed in the bacterium Escherichia coli during anaerobic growth, contains an iron sulfur center. The active form of the enzyme contains an oxygen-sensitive glycyl (1-amino-2-oxoethan-1-yl) radical that is generated by the activating enzyme NrdG via chemistry involving S-adenosylmethionine (SAM) and a [4Fe-4S] cluster. The glycyl radical is 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 gains an electron from a cysteine residue and a proton from formic acid, forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl (1lambda4-disulfan-1-yl) radical bridge between methionine and cysteine residues. Oxidation of formate by the thiosulfuranyl radical results in the release of CO2 and regeneration of the thiyl radical. cf. EC 1.17.4.1, ribonucleoside-diphosphate reductase and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
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Word Map
- 1.1.98.6
-
glycyl
- s-adenosylmethionine
- formate-lyase
- deoxyribonucleotides
-
oxygen-sensitive
- flavodoxins
- adomet
-
2,3-aminomutase
- coproporphyrinogen
-
radical-based
-
thiyl
-
homolytic
- benzylsuccinate
-
datp-sepharose
- medicine
The enzyme appears in viruses and cellular organisms
Reaction Schemes
ribonucleoside 5'-triphosphate
+
=
+
+
Synonyms
anaerobic ribonucleoside-triphosphate reductase, anaerobic ribonucleotide reductase, class III ribonucleoside-triphosphate reductase, nrdD, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
anaerobic ribonucleotide reductase
class III ribonucleoside-triphosphate reductase
nrdD
anaerobic ribonucleotide reductase
-
-
-
-
class III ribonucleoside-triphosphate reductase
-
-
-
-
nrdD
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-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ribonucleoside 5'-triphosphate + formate = 2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O
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-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
ribonucleoside-5'-triphosphate:formate 2'-oxidoreductase
The enzyme, which is expressed in the bacterium Escherichia coli during anaerobic growth, contains an iron sulfur center. The active form of the enzyme contains an oxygen-sensitive glycyl (1-amino-2-oxoethan-1-yl) radical that is generated by the activating enzyme NrdG via chemistry involving S-adenosylmethionine (SAM) and a [4Fe-4S] cluster. The glycyl radical is 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 gains an electron from a cysteine residue and a proton from formic acid, forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl (1lambda4-disulfan-1-yl) radical bridge between methionine and cysteine residues. Oxidation of formate by the thiosulfuranyl radical results in the release of CO2 and regeneration of the thiyl radical. cf. EC 1.17.4.1, ribonucleoside-diphosphate reductase and EC 1.17.4.2, ribonucleoside-triphosphate reductase (thioredoxin).
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ribonucleoside 5'-triphosphate + formate
2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O
CTP + formate
dCTP + CO2 + H2O
-
reaction requires both proteins NrdD and NrdG and occurs in two strictly anaerobic steps. During the first step NrdD is activated by S-adenosylmethionine and deazaflavin plus light in a time-dependent reaction. In the second step the actual reduction of CTP by activated NrdD requires dithiothreitol, formate, KCl, and ATP
-
?
ribonucleoside 5'-triphosphate + formate
2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O
-
-
-
-
?
ribonucleoside 5'-triphosphate + formate
2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O
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in its active form, the enzyme contains an iron-sulfur center and an oxygen-sensitive glycyl radical (Gly681). The radical is generated in the inactive protein from S-adenosylmethionine by an auxiliary enzyme system. During catalysis, formate is stoichiometrically oxidized to CO2, and isotope from [3H]formate appears in water
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?
additional information
?
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-
activation of enzyme involves generation of a specific amino acid free radical that is dependent on a reduced Fe-S cluster and S-adenosylmethionine
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-
?
additional information
?
-
-
reaction with CTP (substrate) and ATP (allosteric effector) in the absence of formate leads to loss of the glycyl radical concomitant with stoichiometric formation of a new radical species and a trapped cytidine derivative that can break down to cytosine. Addition of formate to the new species results in recovery of 80% of the glycly radical and reduction of the cytidine derivative, proposed to be 3'-keto-deoxycytidine, to dCTP and a small amount of cytosine. The structure of the new radical is a thiosulfuranyl [RSSR2] radical, composed of a cysteine thiyl radical stabilized by an interaction with a methionine residue
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-
?
additional information
?
-
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the enzyme reduces ribonucleotides at a low basal rate. Reduction is stimulated up to 10fold by an appropriate modulator (dGTP for ATP reduction, ATP for CTP and UTP reduction, and dlTP for GTP reduction). The enzyme has one class of sites that binds ATP and dATP and regulates pyrimidine ribonucleotide reduction, and another class that binds dATP, dGTP, and dTTP and regulates purine ribonucleotide reduction
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?
additional information
?
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no significant UTP reduction under the conditions used
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-
?
additional information
?
-
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no significant UTP reduction under the conditions used
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-
?
additional information
?
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the enzyme displays two nucleotide-binding sites. One site exhibits half-maximal saturation at approximately 5 mM 8-azidoadenosine 5'-triphosphate, whereas the other site requires 45 microM. The higher affinity site corresponds to residues 289-291 and the other site to the region to residues 147-160. Photoinsertion of 8-azidoadenosine 5'-triphosphate into the site corresponding to residues 147-160 is almost completely abolished when 100 mM dATP, dGTP, or dTTP is included in the photolabeling reaction mixture, whereas 100 mM ATP, GTP, CTP, or dCTP have virtually no effect
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-
?
additional information
?
-
-
the enzyme displays two nucleotide-binding sites. One site exhibits half-maximal saturation at approximately 5 mM 8-azidoadenosine 5'-triphosphate, whereas the other site requires 45 microM. The higher affinity site corresponds to residues 289-291 and the other site to the region to residues 147-160. Photoinsertion of 8-azidoadenosine 5'-triphosphate into the site corresponding to residues 147-160 is almost completely abolished when 100 mM dATP, dGTP, or dTTP is included in the photolabeling reaction mixture, whereas 100 mM ATP, GTP, CTP, or dCTP have virtually no effect
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-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
iron-sulfur centre
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activation of enzyme involves generation of a specific amino acid free radical that is dependent on a reduced Fe-S cluster and S-adenosylmethionine
S-adenosyl-L-methionine
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activation of enzyme involves generation of a specific amino acid free radical that is dependent on a reduced Fe-S cluster and S-adenosylmethionine
S-adenosyl-L-methionine
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S-adenosyl-L-methionine is directly reduced by the Fe-S center of the small subunits during the activation of the enzyme, resulting in methionine and glycyl radical formation. S-adenosyl-L-methionine binds to the small subunits with a Kd of 10 microM and a 1:1 stoichiometry. Dithiothreitol triggers the cleavage of S-adenosyl-L-methionine, leading glycyl radical formation. 3 methionines are formed per mol of protein
S-adenosyl-L-methionine
S-adenosylmethionine together with a metal participates in the generation of the radical required for the reduction of carbon 2' of the ribosyl moiety of CTP
[4Fe-4S]-center
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S-adenosyl-L-methionine is directly reduced by the Fe-S center of the small subunits during the activation of the enzyme
[4Fe-4S]-center
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the 17.5-kDa subunit contains a 4Fe-4S cluster that joins two peptides in a 35-kDa small homodimer (beta2)
[4Fe-4S]-center
the [4Fe-4S]+ form is extremely sensitive to oxygen and converted to [4Fe-4S]2+, [3Fe-4S]+/0, and to the stable [2Fe-2S]2+ form. The oxidized protein retains full activity. The [2Fe-2S] form of the protein can be converted into a [3Fe-4S] form during chromatography on dATP-Sepharose
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
iron-sulfur center
in its active form, the enzyme contains an iron-sulfur center and an oxygen-sensitive glycyl radical (Gly681)
Zn
C-terminal region contains a Zn(Cys)4 center. Residues Cys543, Cys546, Cys561, and Cys564 coordinate the metal ion tetrahedrally
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
1.5 mM, 500fold increase in reduction rate of CTP, 2.5fold increase for GTP
dGTP
1.5 mM, 20fold increase in reduction rate of ATP
dTTP
1.5 mM, 3fold increase in reduction rate of GTP
additional information
enzyme has a single type of allosteric site to which dGTP, dTTP, dATP, and ATP bind competitively
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additional information
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enzyme has a single type of allosteric site to which dGTP, dTTP, dATP, and ATP bind competitively
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additional information
allosteric effectors bind to two separate sites on NrdD, one binding dATP, dGTP, and dTTP and the other binding dATP and ATP. The two sites show an unusually high degree of cooperativity with complex interactions between effectors and a fine-tuning of their physiological effects
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4
ATP
-
presence of dGTP, pH not specified in the publication, temperature not specified in the publication
1
UTP
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presence of ATP, pH not specified in the publication, temperature not specified in the publication
0.05
CTP
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presence of ATP, pH not specified in the publication, temperature not specified in the publication
0.5
CTP
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presence of ATP, pH not specified in the publication, temperature not specified in the publication
0.06
GTP
-
presence of dTTP, pH not specified in the publication, temperature not specified in the publication
0.4
GTP
-
presence of dTTP, pH not specified in the publication, temperature not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.012
dATP
-
substrate ATP, pH not specified in the publication, temperature not specified in the publication
0.05
dTTP
-
substrate GTP, pH not specified in the publication, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
10.5
mutant N78D, pH 8.0, temperature not specified in the publication
11.8
mutant N78C, pH 8.0, temperature not specified in the publication
1155
wild-type, pH 8.0, temperature not specified in the publication
207
mutant N311A, pH 8.0, temperature not specified in the publication
3.6
mutant N78A/N311A, pH 8.0, temperature not specified in the publication
370
substrate CTP, pH not specified in the publication, temperature not specified in the publication
5.6
mutant N311C, pH 8.0, temperature not specified in the publication
575
substrate CTP, presence of ATP, pH not specified in the publication, temperature not specified in the publication
730
substrate CTP, presence of dATP, pH not specified in the publication, temperature not specified in the publication
87.6
mutant N78A, pH 8.0, temperature not specified in the publication
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
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during the reduction of ribonucleotides with [3H]formate tritium appears in water and not in the product deoxyribonucleotide. In D2O, deuterium replaces the OH-group at carbon-2' with retention of configuration. Class I, II and class III enzymes catalyze identical reactions. Members of the three classes of reductases apparently use the same chemical mechanism in spite of having completely different protein structures
physiological function
protein NrdD contains catalytic and allosteric sites and, in its active form, a stable glycyl radical. This radical is generated by NrdG with its [4Fe-4S] cluster and S-adenosylmethionine. NrdD and NrdG anaerobically form a tight alpha2beta2 complex. NrdD alone catalyzes the reduction of CTP with formate as the electron donor and ATP as the allosteric effector. The reaction requires Mg+ and is stimulated by K+ but not by dithiothreitol. NrdD is the actual reductase, and NrdG is an activase
physiological function
proteins NrdG and NrdD together catalyze the reduction of ribonucleoside triphosphates to the corresponding deoxyribonucleotides in the presence of S-adenosylmethionine, reduced flavodoxin or reduced deazaflavin, potassium ions, dithiothreitol, and formate. A [4Fe-4S] cluster is present in reduced NrdG and a glycyl radical in activated NrdD. The two polypeptides of NrdD and the proteins in the NrdD-NrdG complex are only loosely associated. NrdDG is required for strict anaerobic growth of Lactococcus lactis
physiological function
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the enzyme is the actual ribonucleoside triphosphate reductase in the oxygen-sensitive ribonucleoside triphosphate reductase system. The reaction requires an auxiliary protein dA1 of 29000 Da, S-adenosylmethionine, NADPH (with NADH as a less active substitute), dithinthreitol, and magnesium ions, and is strongly stimulated by ATP
Show AA Sequence and Transmembrane Helices (142 entries)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
x * 84100, calculated, x * 74000 and x * 84000, due to truncation of protein at the site of the glycyl radical, SDS-PAGE
heterotetramer
-
2 * 17500, small subunit alpha, plus 2 * 80000, large subunit beta
additional information
additional information
-
occurence of a degradation product named beta2 of 74000 Da
additional information
-
the large and the small proteins form a tight complex with 1:1 stoichiometry. The anaerobic reductase thus has an alpha2beta2 structure
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
quantum chemical calculation of reaction mechanism. Carbon dioxide is formed from formate, which is present as a cofactor. The formate first forms a formyl radical. The next step, where the formyl radical protonates the 3'-keto group of the substrate, is rate limiting with a calculated total barrier of 19.9 kcal/mol, in reasonable agreement with the experimental rate-limiting barrier of 17 kcal/mol. Zero-point and entropy effects are quite significant in lowering the barrier
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C-terminal region contains a Zn(Cys)4 center structurally related to the zinc ribbon motif and to rubredoxin and rubrerythrin. Residues Cys543, Cys546, Cys561, and Cys564 coordinate the metal ion tetrahedrally
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C644A
mutation in a residue of the Zn(Cys)4 center, almost complete loss of activity due to inability to generate the catalytically essential glycyl radical
C647A
mutation in a residue of the Zn(Cys)4 center, almost complete loss of activity due to inability to generate the catalytically essential glycyl radical
C662A
mutation in a residue of the Zn(Cys)4 center, almost complete loss of activity due to inability to generate the catalytically essential glycyl radical
C665A
mutation in a residue of the Zn(Cys)4 center, almost complete loss of activity due to inability to generate the catalytically essential glycyl radical
C260S
activity comparable to wild-type, mutant is able to undergo truncation at the site of the glycyl radical when the radical-containing enzyme is exposed to oxygen
C290S
C453S
activity comparable to wild-type, mutant is able to undergo truncation at the site of the glycyl radical when the radical-containing enzyme is exposed to oxygen
C579S
mutant is able to undergo truncation at the site of the glycyl radical when the radical-containing enzyme is exposed to oxygen
C79S
residue participates in the actual reduction of the substrate. Mutant is able to undergo truncation at the site of the glycyl radical when the radical-containing enzyme is exposed to oxygen
G580A
oxygen-dependent cleavage is not possible in this mutant since no radical can be formed at Ala580
C290S
mutation in conserved residua, less than 10% of wild-type activity
C290S
residue participates in the reaction mechanism by forming a transient thiyl radical. Mutant is able to undergo truncation at the site of the glycyl radical when the radical-containing enzyme is exposed to oxygen
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
medicine
ribonucleotide reductase class III is a virulence determinant in the pathogenesis of staphylococcal arthritis. Mice inoculated with the wild-type strain display significantly more severe arthritis, with significantly more synovitis and destruction of the bone and cartilage versus mice inoculated with a NrdDG mutant strain. The persistence of bacteria in the kidneys is significantly more pronounced in the group inoculated with the wild-type strain
medicine
-
ribonucleotide reductase class III is a virulence determinant in the pathogenesis of staphylococcal arthritis. Mice inoculated with the wild-type strain display significantly more severe arthritis, with significantly more synovitis and destruction of the bone and cartilage versus mice inoculated with a NrdDG mutant strain. The persistence of bacteria in the kidneys is significantly more pronounced in the group inoculated with the wild-type strain
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Logan, D.T.; Mulliez, E.; Larsson, K.M.; Bodevin, S.; Atta, M.; Garnaud, P.E.; Sjberg, B.M.; Fontecave, M.
A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase
Proc. Natl. Acad. Sci. USA
100
3826-3831
2003
Escherichia virus T4 (P07071), Escherichia virus T4, Escherichia coli (P28903), Escherichia coli
brenda
Eliasson, R.; Reichard, P.; Mulliez, E.; Ollagnier, S.; Fontecave, M.; Liepinsh, E.; Otting, G.
The mechanism of the anaerobic Escherichia coli ribonucleotide reductase investigated with nuclear magnetic resonance spectroscopy
Biochem. Biophys. Res. Commun.
214
28-35
1995
Escherichia coli
brenda
Wei, Y.; Mathies, G.; Yokoyama, K.; Chen, J.; Griffin, R.; Stubbe, J.
A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase
J. Am. Chem. Soc.
136
9001-9013
2014
Escherichia coli
brenda
Eliasson, R.; Pontis, E.; Fontecave, M.; Gerez, C.; Harder, J.; Joernvall, H.; Krook, M.; Reichard, P.
Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli
J. Biol. Chem.
267
25541-25547
1992
Escherichia coli
brenda
Mulliez, E.; Fontecave, M.; Gaillard, J.; Reichard, P.
An iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli
J. Biol. Chem.
268
2296-2299
1993
Escherichia coli
brenda
Eliasson, R.; Pontis, E.; Sun, X.; Reichard, P.
Allosteric control of the substrate specificity of the anaerobic ribonucleotide reductase from Escherichia coli
J. Biol. Chem.
269
26052-26057
1994
Escherichia coli
brenda
Ollagnier, S.; Mulliez, E.; Gaillard, J.; Eliasson, R.; Fontecave, M.; Reichard, P.
The anaerobic Escherichia coli ribonucleotide reductase. Subunit structure and iron sulfur center
J. Biol. Chem.
271
9410-9416
1996
Escherichia coli
brenda
Ollagnier, S.; Mulliez, E.; Schmidt, P.P.; Eliasson, R.; Gaillard, J.; Deronzier, C.; Bergman, T.; Graeslund, A.; Reichard, P.; Fontecave, M.
Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction
J. Biol. Chem.
272
24216-24223
1997
Escherichia coli
brenda
Olcott, M.C.; Andersson, J.; Sjoeberg, B.M.
Localization and characterization of two nucleotide-binding sites on the anaerobic ribonucleotide reductase from bacteriophage T4
J. Biol. Chem.
273
24853-24860
1998
Escherichia virus T4 (P07071), Escherichia virus T4
brenda
Andersson, J.; Westman, M.; Hofer, A.; Sjoberg, B.M.
Allosteric regulation of the class III anaerobic ribonucleotide reductase from bacteriophage T4
J. Biol. Chem.
275
19443-19448
2000
Escherichia virus T4 (P07071), Escherichia virus T4
brenda
Andersson, J.; Westman, M.; Sahlin, M.; Sjoberg, B.M.
Cysteines involved in radical generation and catalysis of class III anaerobic ribonucleotide reductase. A protein engineering study of bacteriophage T4 NrdD
J. Biol. Chem.
275
19449-19455
2000
Escherichia virus T4 (P07071), Escherichia virus T4
brenda
Torrents, E.; Eliasson, R.; Wolpher, H.; Graeslund, A.; Reichard, P.
The anaerobic ribonucleotide reductase from Lactococcus lactis. Interactions between the two proteins NrdD and NrdG
J. Biol. Chem.
276
33488-33494
2001
Lactococcus lactis subsp. cremoris (Q9ZAX6)
brenda
Mulliez, E.; Ollagnier-de Choudens, S.; Meier, C.; Cremonini, M.; Luchinat, C.; Trautwein, A.X.; Fontecave, M.
Iron-sulfur interconversions in the anaerobic ribonucleotide reductase from Escherichia coli
J. Biol. Inorg. Chem.
4
614-620
1999
Escherichia coli (P28903), Escherichia coli
brenda
Cho, K.; Himo, F.; Grslund, A.; Siegbahn, P.
The substrate reaction mechanism of class III anaerobic ribonucleotide reductase
J. Phys. Chem. B
105
6445-6452
2001
Escherichia coli
-
brenda
Kirdis, E.; Jonsson, I.M.; Kubica, M.; Potempa, J.; Josefsson, E.; Masalha, M.; Foster, S.J.; Tarkowski, A.
Ribonucleotide reductase class III, an essential enzyme for the anaerobic growth of Staphylococcus aureus, is a virulence determinant in septic arthritis
Microb. Pathog.
43
179-188
2007
Staphylococcus aureus (A0A0H3KJ34), Staphylococcus aureus Newman (A0A0H3KJ34)
brenda
Eliasson, R.; Fontecave, M.; Jornvall, H.; Krook, M.; Pontis, E.; Reichard, P.
The anaerobic ribonucleoside triphosphate reductase from Escherichia coli requires S-adenosylmethionine as a cofactor
Proc. Natl. Acad. Sci. USA
87
3314-3318
1990
Escherichia coli (P28903)
brenda
Mulliez, E.; Ollagnier, S.; Fontecave, M.; Eliasson, R.; Reichard, P.
Formate is the hydrogen donor for the anaerobic ribonucleotide reductase from Escherichia coli
Proc. Natl. Acad. Sci. USA
92
8759-8762
1995
Escherichia coli (P28903), Escherichia coli
brenda
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