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Information on EC 1.17.4.2 - ribonucleoside-triphosphate reductase (thioredoxin) and Organism(s) Lactobacillus leichmannii and UniProt Accession Q59490
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1.17.4.2 ribonucleoside-triphosphate reductase (thioredoxin)IUBMB Comments
The enzyme, characterized from the bacterium Lactobacillus leichmannii, is similar to class II ribonucleoside-diphosphate reductase (cf. EC 1.17.4.1). However, it is specific for the triphosphate versions of its substrates. The enzyme contains an adenosylcobalamin cofactor that is involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue. This radical 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).
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Word Map
- 1.17.4.2
- hydroxyurea
- deoxyribonucleotides
- dntp
- rr
- herpes
-
tyrosyl
- simplex
- gemcitabine
- leukemia
- reductases
- thymidine
- thioredoxins
- deoxycytidine
-
deoxynucleotides
- cdp
-
s-phase
- thymidylate
- thiosemicarbazone
- glutaredoxins
-
checkpoint
-
nsclc
- cytidine
-
diferric
- deoxyadenosine
-
diiron
-
fork
- deoxyguanosine
- 5'-diphosphate
-
nonidentical
- gallium
-
antiferromagnetically
-
hyperfine
-
proton-coupled
-
dinuclear
-
oncolytic
-
cross-complementation
- acyclovir
- cladribine
- chk1
-
thiyl
- aphidicolin
-
cross-complementing
-
endor
- fludarabine
-
b12-dependent
-
gemcitabine-based
- deoxythymidine
- analysis
-
gemcitabine-induced
-
high-valent
-
peroxo
The taxonomic range for the selected organisms is: Lactobacillus leichmannii
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
ribonucleotide reductase, rtpr, class ib rnr, ribonucleoside triphosphate reductase, class ii rnr, class iii rnr, class ib ribonucleotide reductase, ribonucleotide diphosphate reductase, class iii ribonucleotide reductase, class ii ribonucleotide reductase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
adenosylcobalamin-dependent ribonucleoside-triphosphate reductase
-
2'-deoxyribonucleoside-triphosphate:oxidized-thioredoxin 2'-oxidoreductase
-
-
-
-
ribonucleoside triphosphate reductase
ribonucleotide reductase
ribonucleoside triphosphate reductase
-
-
-
-
ribonucleotide reductase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
2'-deoxyribonucleoside-5'-triphosphate:thioredoxin-disulfide 2'-oxidoreductase
The enzyme, characterized from the bacterium Lactobacillus leichmannii, is similar to class II ribonucleoside-diphosphate reductase (cf. EC 1.17.4.1). However, it is specific for the triphosphate versions of its substrates. The enzyme contains an adenosylcobalamin cofactor that is involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue. This radical 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).
CAS REGISTRY NUMBER
COMMENTARY
9068-66-0
-
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
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
ribonucleoside triphosphate + reduced thioredoxin
-
-
-
-
r
ATP + reduced thioredoxin
dATP + oxidized thioredoxin + H2O
-
-
-
-
?
CTP + reduced thioredoxin
dCTP + oxidized thioredoxin + H2O
-
-
-
-
?
GTP + reduced thioredoxin
dGTP + oxidized thioredoxin + H2O
-
-
-
-
?
ribonucleoside triphosphate + dihydrolipoate
2'-deoxyribonucleoside triphosphate + lipoate + H2O
-
-
-
-
?
ribonucleoside triphosphate + dithioerythritol
2'-deoxyribonucleoside triphosphate + ? + H2O
-
-
-
-
?
ribonucleoside triphosphate + dithiothreitol
2'-deoxyribonucleoside triphosphate + ? + H2O
-
-
-
-
?
ribonucleoside triphosphate + reduced thioredoxin
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
-
437887, 437888, 437889, 437890, 437891, 437892, 437893, 437894, 437896, 437897, 437898, 437899, 437900, 437901, 437902, 437903
-
-
r
ribonucleoside triphosphate + reduced thioredoxin
deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
-
-
-
?
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
UTP + reduced thioredoxin
dUTP + oxidized thioredoxin + H2O
-
-
-
-
?
ADP + reduced thioredoxin
dADP + oxidized thioredoxin + H2O
-
-
-
-
?
ADP + reduced thioredoxin
dADP + oxidized thioredoxin + H2O
-
most active diphosphate substrate
-
-
?
CDP + reduced thioredoxin
dCDP + oxidized thioredoxin + H2O
-
-
-
-
?
CDP + reduced thioredoxin
dCDP + oxidized thioredoxin + H2O
-
poorly reduced
-
-
?
CMP + reduced thioredoxin
dCMP + oxidized thioredoxin + H2O
-
-
-
-
?
CMP + reduced thioredoxin
dCMP + oxidized thioredoxin + H2O
-
poorly reduced
-
-
?
GDP + reduced thioredoxin
dGDP + oxidized thioredoxin + H2O
-
-
-
-
?
GDP + reduced thioredoxin
dGDP + oxidized thioredoxin + H2O
-
poorly reduced
-
-
?
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
-
437887, 437889, 437890, 437891, 437892, 437893, 437894, 437896, 437897, 437898, 437899, 437901, 437902, 437903
-
-
r
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
physiological hydrogen donor is unknown
-
-
r
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
catalyzes the rate-determining step in DNA biosynthesis
-
-
r
UDP + reduced thioredoxin
dUDP + oxidized thioredoxin + H2O
-
-
-
-
?
UDP + reduced thioredoxin
dUDP + oxidized thioredoxin + H2O
-
poorly reduced
-
-
?
additional information
?
-
-
the enzyme also catalyzes the exchange of the C5'-hydrogens of adenosylcobalamin with solvent hydrogen, epimerization of the (5'S)-[5'-2H1]- and (5'R)-[5'-2H1]-isotopomers of adenosylcobalamin
-
-
?
additional information
?
-
-
RTPR catalyzes the conversion of nucleoside triphosphates to deoxynucleotides requiring adenosylcobalamin as a cofactor, model of reaction mechanism, overview
-
-
?
additional information
?
-
-
RTPR catalyzes the conversion of nucleoside triphosphates to deoxynucleotides using adenosylcobalamin as a cofactor
-
-
?
NATURAL SUBSTRATE
NATURAL 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
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
ribonucleoside triphosphate + reduced thioredoxin
-
-
-
-
r
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
-
437887, 437889, 437890, 437891, 437892, 437893, 437894, 437896, 437897, 437898, 437899, 437901, 437902, 437903
-
-
r
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
physiological hydrogen donor is unknown
-
-
r
ribonucleoside triphosphate + reduced thioredoxin + H2O
2'-deoxyribonucleoside triphosphate + oxidized thioredoxin + H2O
-
catalyzes the rate-determining step in DNA biosynthesis
-
-
r
additional information
?
-
-
RTPR catalyzes the conversion of nucleoside triphosphates to deoxynucleotides requiring adenosylcobalamin as a cofactor, model of reaction mechanism, overview
-
-
?
additional information
?
-
-
RTPR catalyzes the conversion of nucleoside triphosphates to deoxynucleotides using adenosylcobalamin as a cofactor
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
adenosylcobalamin
in the course of catalysis, the protein active site presents the reacting molecules with an environment that includes a hydrogen bond to the thiyl radical and intervening residues or solvent mediating an exchange coupling between the thiyl radical and cob(II)alamin
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
-
enzyme requires adenosylcobalamin as a cofactor, the Co ion is involved in the reaction
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2',2'-difluoro-2'-deoxycytidine 5'-triphosphate
-
complete inactivation of the enzyme by 1 equiv of 2',2'-difluoro-2'-deoxyCTP, F2CTP, in about 2 min proceeding via alkylation by the sugar of F2CTP and AdoCbl destruction. 0.47 equiv of a sugar moiety is covalently bound to RNR and 0.25 equiv of a cobalt(III) corrin is tightly associated, likely through a covalent interaction with C419 (Co-S) in the active site of RNR. Analysis of the relationship of the nonalkylative pathway for RNR inactivation relative to the alkylative pathway, overview
2',2'-difluoro-2'-deoxycytidine 5'-triphosphate
-
F2CTP, a clinically used anti-cancer drug, synthesis, overview. Causes rapid enzyme inactivation through covalent modification, mechanism of inactivation, analysis by mass spectrometry and radio- or deuterium-labeled compounds, overview. C119 is involved in the reaction
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
dGTP
-
both epimerization and 5'-hydrogen exchange reactions are stimulated by the allosteric effector
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
69300
-
enzyme in 6 M guanidine-HCl, 0.1 M dithiothreitol, equilibrium ultracentrifugation
72500
-
native enzyme in 0.1 M glycine buffer, pH 9.1, equilibrium ultracentrifugation
72600
-
maleated enzyme in 0.05 M phosphate buffer, equilibrium ultracentrifugation
74500
-
enzyme in 6 M guanidine-HCl, 0.1 M dithiothreitol, heated for 20 min at 60°C, equilibrium ultracentrifugation
75300
-
native enzyme in 0.05 M phosphate buffer, pH 7.0, sedimentation equilibrium method
76000
81850
-
predicted molecular weight based on the predicted amino acid sequence from the sequenced gene
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C408A
-
only wild-type enzyme catalyzes epimerization of the (5'S)-[5'-2H1]- and (5'R)-[5'-2H1]-isotopomers of adenosylcobalamin, no activity of mutant enzyme
C408S
-
only wild-type enzyme catalyzes epimerization of the (5'S)-[5'-2H1]- and (5'R)-[5'-2H1]-isotopomers of adenosylcobalamin, no activity of mutant enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
fairly stable under conditions of storage, losing only about 23% of its activity in 15 months
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-100°C, may be stored as frozen paste for at least 3 months without significant loss of activity
-
-20°C, crude extracts relatively unstable, most of the activity disappears within a few weeks
-
-65°C, no detectable loss of enzyme has been observed during several years of storage of packed bacteria
-
0-4°C, acetone and hydroxylapatite fractions are quite stable, at least 70-80% of their activities remain after 3 months
-
0-4°C, crude extracts relatively unstable, most of the activity disappears within a few weeks
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
development of a rapid freeze-quench apparatus for the preparation of millisecond quench time rapid freeze-quench samples which can be packed into small sample tubes used for continuous-wave and pulsed high-frequency electron paramagnetic resonance spectroscopy
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bakley, R.L.
Cobamides and ribonucleotide reduction. I. Cobamide stimulation of ribonucleotide reduction in extracts of Lactobacillus leichmannii
J. Biol. Chem.
240
2173-2180
1965
Lactobacillus leichmannii
Goulian, M.; Beck, W.S.
Purification and properties of cobamide-dependent ribonucleotide reductase from Lactobacillus leichmannii
J. Biol. Chem.
241
4233-4242
1966
Lactobacillus leichmannii
Sando, G.N.; Hogenkamp, H.P.C.
Ribonucleotide reductase from Thermus X-1, a thermophilic organism
Biochemistry
12
3316-3322
1973
Lactobacillus leichmannii, Thermus aquaticus, Thermus sp., Thermus sp. X-1, Thermus aquaticus YT-1
Chen, A.K.; Bhan, A.; Hopper, S.; Abrams, R.; Franzen, J.S.
Substrate and effector binding to ribonucleoside triphosphate reductase of Lactobacillus leichmannii
Biochemistry
13
654-661
1974
Lactobacillus leichmannii
Hamilton, F.D.
Ribonucleotide reductase from Euglena gracilis. A 5-deoxyadenoslycobalamin-dependent enzyme
J. Biol. Chem.
249
4428-4434
1974
Escherichia coli, Euglena gracilis, Lactobacillus leichmannii, Euglena gracilis Z
Blakley, R.L.
Ribonucleoside triphosphate reductase from Lactobacillus leichmannii
Methods Enzymol.
51
246-259
1978
Astasia sp., Clostridium sp., Corynebacterium sp., Euglena sp., Lactobacillus leichmannii, Pseudomonas sp., Rhizobium sp.
Gleason, F.K.; Frick, T.D.
Adenosylcobalamin-dependent ribonucleotide reductase from the blue-green alga, Anabaena sp. Purification and partial characterization
J. Biol. Chem.
255
7728-7733
1980
Anabaena sp., Escherichia coli, Lactobacillus leichmannii, Anabaena sp. 7119
Ashley, G.W.; Harris, G.; Stubbe, J.
The mechanism of Lactobacillus leichmannii ribonucleotide reductase. Evidence for 3 carbon-hydrogen bond cleavage and a unique role for coenzyme B12
J. Biol. Chem.
261
3958-3964
1986
Lactobacillus leichmannii
Booker, S.; Licht, S.; Broderick, J.; Stubbe, J.
Coenzyme B12-dependent ribonucleotide reductase: evidence for the participation of five cysteine residues in ribonucleotide reduction
Biochemistry
33
12676-12685
1994
Lactobacillus leichmannii
Jordan, A.; Torrents, E.; Jeanthon, C.; Eliasson, R.; Hellman, U.; Wernstedt, C.; Barbe, J.; Gibert, I.; Reichard, P.
B12-dependent ribonucleotide reductases from deeply rooted eubacteria are structurally related to the aerobic enzyme from Escherichia coli
Proc. Natl. Acad. Sci. USA
94
13487-13492
1997
Archaeoglobus fulgidus, Chloroflexus aurantiacus, Deinococcus radiodurans, Escherichia coli, Lactobacillus leichmannii, Methanocaldococcus jannaschii, Mycobacterium tuberculosis, Pyrococcus furiosus, Thermoplasma acidophilum, Thermotoga maritima, Deinococcus radiodurans R1 / ATCC 13939 / DSM 20539, Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
Tauer, A.; Benner, S.A.
The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum
Proc. Natl. Acad. Sci. USA
94
53-58
1997
Anabaena sp., Escherichia coli, Halobacterium salinarum, Haloferax volcanii, Homo sapiens, Lactobacillus leichmannii, Mycobacterium tuberculosis, Thermoplasma acidophilum, Thermus aquaticus, Thermus aquaticus X1
Jordan, A.; Torrents, E.; Sala, I.; Hellman, U.; Gibert, I.; Reichard, P.
Ribonucleotide reduction in Pseudomonas species: simultaneous presence of active enzymes from different classes
J. Bacteriol.
181
3974-3980
1999
Brevundimonas diminuta, Brevundimonas vesicularis, Burkholderia cepacia, Delftia acidovorans, Deinococcus radiodurans, Escherichia coli, Hydrogenophaga flava, Lactobacillus leichmannii, Paracoccus denitrificans, Mycobacterium tuberculosis, Pseudomonas sp., Pseudomonas aeruginosa, Pseudomonas putida, Stenotrophomonas maltophilia, Pseudomonas stutzeri, Ralstonia pickettii, Xanthomonas campestris
Licht, S.S.; Booker, S.; Stubbe, J.
Studies on the catalysis of carbon-cobalt bond homolysis by ribonucleoside triphosphate reductase: evidence for concerted carbon-cobalt bond homolysis and thiyl radical formation
Biochemistry
38
1221-1233
1999
Escherichia coli, Lactobacillus leichmannii
Licht, S.S.; Lawrence, C.C.; Stubbe, J.
Thermodynamic and kinetic studies on carbon-cobalt bond homolysis by ribonucleoside triphosphate reductase: The importance of entropy in catalysis
Biochemistry
38
1234-1242
1999
Lactobacillus leichmannii
Suto, R.K.; Poppe, L.; Retey, J.; Finke, R.G.
Ribonucleoside triphosphate reductase from Lactobacillus leichmannii: Kinetic evaluation of a series of adenosylcobalamin competitive inhibitors, [omega-(adenosin-5'-O-yl)alkyl]cobalamins, which mimic the post Co-C homolysis intermediate
Bioorg. Chem.
27
451-462
1999
Lactobacillus leichmannii
-
Suto, R.K.; Whalen, M.A.; Finke, R.G.
Adenosylcobalamin-dependent ribonucleoside triphosphate reductase from Lactobacillus leichmannii. Rapid, improved purification involving dGTP-based affinity chromatography plus biophysical characterization studies demonstrating enhanced, crystallographic level purity
Prep. Biochem. Biotechnol.
29
273-309
1999
Lactobacillus leichmannii
Chen, D.; Abend, A.; Stubbe, J.; Frey, P.A.
Epimerization at carbon-5' of (5'R)-[5'-2H]adenosylcobalamin by ribonucleoside triphosphate reductase: cysteine 408-independent cleavage of the Co-C5'-bond
Biochemistry
42
4578-4584
2003
Lactobacillus leichmannii
Lohman, G.J.; Gerfen, G.J.; Stubbe, J.
Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2,2-difluoro-2-deoxycytidine 5-triphosphate: adenosylcobalamin destruction and formation of a nucleotide-based radical
Biochemistry
49
1396-1403
2010
Lactobacillus leichmannii
Lohman, G.J.; Stubbe, J.
Inactivation of Lactobacillus leichmannii ribonucleotide reductase by 2',2'-difluoro-2'-deoxycytidine 5'-triphosphate: covalent modification
Biochemistry
49
1404-1417
2010
Lactobacillus leichmannii
Manzerova, J.; Krymov, V.; Gerfen, G.J.
Investigating the intermediates in the reaction of ribonucleoside triphosphate reductase from Lactobacillus leichmannii: An application of HF EPR-RFQ technology
J. Magn. Reson.
213
32-45
2011
Lactobacillus leichmannii (Q59490), Lactobacillus leichmannii
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