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Information on EC 2.4.2.6 - nucleoside deoxyribosyltransferase and Organism(s) Lactobacillus leichmannii and UniProt Accession Q9R5V5
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2.4.2.6 nucleoside deoxyribosyltransferaseIUBMB Comments
Base1 and base2 represent various purines and pyrimidines.
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Word Map
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
ndrt, nucleoside 2'-deoxyribosyltransferase, trans-n-deoxyribosylase, ctndt, 2'-deoxyribosyltransferase, drtase i, nucleoside 2-deoxyribosyltransferase, nucleoside deoxyribosyltransferase, landt, drtase ii, 
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topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
deoxyribose transferase
-
-
-
-
deoxyribosyltransferase, nucleoside
-
-
-
-
DRTase II
-
catalyzes the transfer of the deoxyribosyl moiety between purines or pyrimidines as well as from a purine to a pyrimidine
NdRT-II
-
-
-
-
NTD
nucleoside 2'-deoxyribosyltransferase
nucleoside trans-N-deoxyribosylase
-
-
-
-
purine(pyrimidine) nucleoside:purine(pyrimidine) deoxyribosyl transferase
-
-
-
-
trans-deoxyribosylase
-
-
-
-
trans-N-deoxyribosylase
-
-
-
-
trans-N-glycosidase
-
-
-
-
transdeoxyribosylase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1
reaction mechanism with oxocarbenium ion as the reaction intermediate, overview
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pentosyl group transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
SYSTEMATIC NAME
IUBMB Comments
nucleoside:purine(pyrimidine) deoxy-D-ribosyltransferase
Base1 and base2 represent various purines and pyrimidines.
CAS REGISTRY NUMBER
COMMENTARY
9026-86-2
-
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'-deoxyadenosine + 5-fluorouracil
2'-deoxy-D-ribosyl-5-fluorouracil + adenine
reaction is catalyzed by mutants F13R/D92S/N123S and F13Q/D92S/N123S
-
-
?
2'-deoxycytidine + 2,6-diaminopurine
2,6-diaminopurine 2-deoxy-D-riboside + cytosine
reaction is catalyzed by mutants F13R/D92S/N123S and F13Q/D92S/N123S
-
-
?
2'-deoxycytidine + 5-bromouracil
2'-deoxy-5-bromouridine + cytosine
reaction is catalyzed by mutants F13R/D92S/N123S and F13Q/D92S/N123S
-
-
?
2'-deoxycytidine + 6-chloropurine
6-chloropurine 2-deoxy-D-ribose 5-phosphate + cytosine
reaction is catalyzed by mutants F13R/D92S/N123S and F13Q/D92S/N123S
-
-
?
2'-deoxycytidine + adenine
2'-deoxyadenosine + cytosine
-
-
-
?
2'-deoxyinosine + adenine
2'-deoxyadenosine + hypoxanthine
-
-
-
?
dCMP + 2,6-dichloropurine
2,6-dichloropurin-9-yl-2'-deoxy-beta-D-ribose 5'-phosphate + cytosine
reaction is catalyzed by mutants F13R/D92S/N123S and F13Q/D92S/N123S
-
-
?
2',3'-dideoxycytidine + adenine
2',3'-dideoxyadenosine + cytosine
-
-
-
?
2',3'-dideoxycytidine + hypoxanthine
2',3'-dideoxyinosine + cytosine
-
-
-
?
2',3'-dideoxyguanosine + thymine
2',3'-dideoxythymidine + guanine
-
-
-
?
2',3'-dideoxyinosine + adenine
2',3'-dideoxyadenosine + hypoxanthine
-
-
-
?
2',3'-dideoxythymidine + adenine
2',3'-dideoxyadenosine + thymine
-
-
-
?
2',3'-dideoxyuridine + cytosine
2',3'-dideoxycytidine + uracil
-
-
-
?
2',3'didehydro-2',3'-dideoxythymidine + adenine
2',3'didehydro-2',3'-dideoxyadenosine + thymine
-
-
-
?
2'-deoxycytidine + 6-chloroguanine
cytosine + 2'-deoxy-6-chloroguanosine
-
DRTase II
-
-
?
2'-deoxycytidine + adenine
2'-deoxyadenosine + cytosine
-
-
-
?
2'-deoxycytidine + hypoxanthine
2'-deoxyinosine + cytosine
-
-
-
?
2'-deoxyguanosine + thymine
2'-deoxythymidine + guanine
-
-
-
?
2'-deoxyinosine + adenine
2'-deoxyadenosine + hypoxanthine
-
-
-
?
2'-deoxythymidine + adenine
2'-deoxyadenosine + thymine
-
-
-
?
2'-deoxyuridine + cytosine
2'-deoxycytidine + uracil
-
-
-
?
deoxyadenosine + cytosine
adenine + deoxycytidine
-
DRTase II
-
-
?
deoxycytidine + 1,7-dimethylguanine
cytosine + deoxy-1,7-dimethylguanosine
-
DRTase II
-
-
?
deoxyinosine + 1,7-dimethylguanine
hypoxanthine + deoxy-1,7-dimethylguanosine
-
DRTase I
-
-
?
deoxyinosine + 6-chloroguanine
hypoxanthine + deoxy-6-chloroguanosine
-
DRTase I
-
-
?
deoxyinosine + adenine
hypoxanthine + deoxyadenosine
-
DRTase I
-
-
r
deoxyinosine + cytosine
hypoxanthine + deoxycytidine
-
DRTase II
-
-
?
deoxyinosine + guanine
hypoxanthine + deoxyguanosine
-
DRTase I
-
-
?
thymidine + 2,4-di-tert-butoxy-5-(1H-imidazol-4-yl)pyrimidine
2,4-di-tert-butoxy-5-(1-beta-D-ribofuranosyl-1H-imidazol-4-yl)pyrimidine + thymine
-
-
-
-
?
thymidine + 2-(1H-imidazol-4-yl)benzaldehyde
2-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-benzaldehyde + thymine
-
-
-
-
?
thymidine + 2-fluoro-3-(1H-imidazol-4-yl)pyridine
2-fluoro-3-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-pyridine + thymine
-
-
-
-
?
thymidine + 3-(1H-imidazol-4-yl)pyridine
3-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-pyridine + thymine
-
-
-
-
?
thymidine + 3-bromo-5-(1H-imidazol-4-yl)pyridine
5-bromo-3-[1-(2-deoxy-beta -D-ribofuranosyl)-1H-imidazol-4-yl]-pyridin + thymine
-
-
-
-
?
thymidine + 4-(1-benzofuran-2-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(benzofuran-2-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(1H-imidazol-4-yl)benzonitrile
4-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-benzonitrile + thymine
-
-
-
-
?
thymidine + 4-(2,4-difluorophenyl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(2,4-difluorophenyl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(4-ethoxyphenyl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(4-ethoxyphenyl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(4-methoxyphenyl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(4-methoxyphenyl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(6-methoxynaphthalen-2-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(6-methoxynaphthalen-2-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(dibenzo[b,d]furan-4-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(dibenzo[b,d]furan-4-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-(naphthalen-2-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(naphthalen-2-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-([1,1'-biphenyl]-3-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(biphenyl-3-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-([1,1'-biphenyl]-4-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(biphenyl-4-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-([11,21:23,31-terphenyl]-25-yl)-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-[(3,5-diphenyl)phenyl]-1H-imidazole + thymine
-
-
-
-
?
thymidine + 4-phenyl-1H-imidazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-phenyl-1H-imidazole + thymine
-
-
-
-
?
thymidine + 5-(1H-imidazol-4-yl)-1H-indazole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(1H-indazol-5-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 5-(1H-imidazol-4-yl)-1H-indole
1-(2-deoxy-beta-D-ribofuranosyl)-4-(1H-indol-5-yl)-1H-imidazole + thymine
-
-
-
-
?
thymidine + 5-(1H-imidazol-4-yl)-2,4-dimethoxypyrimidine
2,4-dimethoxy-5-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-pyrimidine + thymine
-
-
-
-
?
thymidine + 5-(1H-imidazol-4-yl)pyrimidin-2-amine
2-amino-5-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-pyrimidine + thymine
-
-
-
-
?
thymidine + 5-(1H-imidazol-4-yl)pyrimidine
5-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-pyrimidine + thymine
-
-
-
-
?
thymidine + 6-methylthio-8-trifluoromethylpurine
thymine + 9-(2-deoxy-beta-D-ribofuranosyl)-6-methylthio-8-trifluoromethylpurine
-
-
-
-
?
thymidine + 8-bromoadenine
thymine + 2'-deoxy-8-bromoadenosine
-
-
-
?
thymidine + 8-chloroadenine
thymine + 2'-deoxy-8-chloroadenosine
-
-
3-deoxyribonucleoside + 9-deoxyribonucleoside
?
thymidine + 8-chlorotheophylline
thymine + 9-(2-deoxy-beta-D-ribofuranosyl)-8-chlorotheophylline
-
-
-
-
?
thymidine + 8-methyladenine
thymine + 2'-deoxy-8-methyladenosine
-
-
-
-
?
thymidine + 8-trifluoromethyladenine
thymine + 2'-deoxy-8-trifluoromethyladenosine
-
-
-
-
?
thymidine + methyl 3-(1H-imidazol-4-yl)benzoate
methyl 3-[1-(2-deoxy-beta-D-ribofuranosyl)-1H-imidazol-4-yl]-benzoate + thymine
-
-
-
-
?
thymidine + [4-(1H-imidazol-4-yl)phenyl]methanol
1-(2-deoxy-beta-D-ribofuranosyl)-4-(4-hydroxymethylphenyl)-1H-imidazole + thymine
-
-
-
-
?
2-deoxy-D-ribosyl-base1 + base2
2-deoxy-D-ribosyl-base2 + base1
-
-
-
?
2-deoxy-D-ribosyl-base1 + base2
2-deoxy-D-ribosyl-base2 + base1
-
-
-
-
?
thymidine + adenine
thymine + 2'-deoxyadenosine
-
-
3-deoxyribonucleoside
?
additional information
?
-
no activity with 3'-azido-3'-deoxythymidine or 3'-amino-3'-deoxythymidine with adenine as acceptor
-
-
?
additional information
?
-
the enzyme accepts purines or pyrimidines as donor substrates, showing preference for 2'-deoxycytidine > 2'-deoxyuridine > 2'-deoxyadenosine and thymidine > 2'-deoxyguanosine >>> 2'-deoxyinosine, and a similar preference for pyrimidines and purines
-
-
?
additional information
?
-
-
DRTase I is strictly specific for transfer between purine bases. DRTase II catalyzes the transfer of the deoxyribosyl moiety between purines or pyrimidines as well as from a purine to a pyrimidine
-
-
?
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-deoxy-D-ribosyl-base1 + base2
2-deoxy-D-ribosyl-base2 + base1
-
-
-
?
2-deoxy-D-ribosyl-base1 + base2
2-deoxy-D-ribosyl-base2 + base1
-
-
-
-
?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.01
0.017
wild-type, with 2',3'-dideoxythymidine and adenine as substrates
0.04
0.056
wild-type, with 2',3'-dideoxyuridine and cytosine as substrates
0.2
mutant G9S, with 2',3'didehydro-2',3'-dideoxythymidine and adenine as substrates
0.25
mutant G9S, with 3'-dideoxythymidine and adenine as substrates
0.4
mutant G9S, with 2',3'-dideoxyguanosine and thymine as substrates
0.47
mutant G9S, with 2'-deoxyinosine and adenine as substrates
0.8
mutant G9S, with 2',3'-dideoxycytidine and hypoxanthine as substrates
1.04
mutant G9S, with 2'-deoxythymidine and adenine as substrates
1.25
mutant G9S, with 2'-deoxycytidine and hypoxanthine as substrates
1.3
mutant G9S, with 2',3'-dideoxyuridine and cytosine as substrates
11.9
wild-type, with 2'-deoxythymidine and adenine as substrates
173
wild-type, with 2'-deoxycytidine and adenine as substrates
27.1
mutant G9S, with 2'-deoxycytidine and adenine as substrates
29
wild-type, with 2',3'-dideoxycytidine and adenine as substrates
3.1
mutant G9S, with 2'-deoxyuridine and cytosine as substrates
3.6
wild-type, with 2'-deoxyinosine and adenine as substrates
42.5
wild-type, with 2'-deoxyuridine and cytosine as substrates
6
mutant G9S, with 2',3'-dideoxycytidine and adenine as substrates
0.01
wild-type, with 2',3'-dideoxyguanosine and thymine as substrates
0.01
wild-type, with 2',3'-dideoxyinosine and adenine as substrates
0.01
wild-type, with 2',3'didehydro-2',3'-dideoxythymidine and adenine as substrates
0.01
wild-type, with 2'-deoxycytidine and hypoxanthine as substrates
0.04
mutant G9S, with 2',3'-dideoxyinosine and adenine as substrates
0.04
wild-type, with 2',3'-dideoxycytidine and hypoxanthine as substrates
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
reaction mechanism of nucleoside 2'-deoxyribosyltransferases, a free-energy landscape supports an oxocarbenium ion as the reaction intermediate. Structure-function analysis of wild-type and mutant enzymes using enzyme crystal structures (PDB IDs 1F8X and 1F8Y), QM/MM MD simulations, overview
additional information
-
reaction mechanism of nucleoside 2'-deoxyribosyltransferases, a free-energy landscape supports an oxocarbenium ion as the reaction intermediate. Structure-function analysis of wild-type and mutant enzymes using enzyme crystal structures (PDB IDs 1F8X and 1F8Y), QM/MM MD simulations, overview
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
110000
18000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
analysis of the crystal structures with PDB IDs 1F8X and 1F8Y
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
G9C
can not improve 2',3'-dideoxyribose transfer reaction, kcat is diminished as compared to wild-type
G9S
G9T
Ser remains a better substituent for Gly-9 than Thr, kcat is diminished as compared to wild-type
G9W
can not improve 2',3'-dideoxyribose transfer reaction, kcat is diminished as compared to wild-type
G9S
-
a single amino-acid substitution allows the conversion of the nucleoside 2'-deoxyribosyltransferase activity to a nucleoside 2',3'-dideoxy- or 2'3'-didehydro, 2',3'-dideoxyribosyltransferase activity
G9S
mutation allows conversion of the nucleoside 2'deoxyribosyltransferase activity to a nucleoside 2',3'-dideoxy- or 2',3'-didehydro,2',3'-dideoxyribosyltransferase activity, kcat is diminished as compared to wild-type
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of the catalytically inactive mutant E98A in Escherichia coli
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Cook, W.J.; Short, S.A.; Ealick, S.E.
Crystallization and preliminary X-ray investigation of recombinant Lactobacillus leichmannii nucleoside deoxyribosyltransferase
J. Biol. Chem.
265
2682-2683
1990
Lactobacillus leichmannii
Huang, M.C.; Montgomery, J.A.; Thorpe, M.C.; Stewart, E.L.; Secrist III, J.A.; Blakley, R.L.
Formation of 3-(2-deoxyribofuranosyl) and 9-(2-deoxyribofuranosyl) nucleosides of 8-substituted purines by nucleoside deoxyribosyltransferase
Arch. Biochem. Biophys.
222
133-144
1983
Lactobacillus leichmannii
Becker, J.; Brendel, M.
Rapid purification and characterization of two distinct N-deoxyribosyltransferases of Lactobacillus leichmannii
Biol. Chem. Hoppe-Seyler
377
357-362
1996
Lactobacillus leichmannii
Porter, D.J.T.; Short, S.A.
Nucleoside 2-deoxyribosyltransferase. Pre-steady-state kinetic analysis of native enzyme and mutant enzyme with an alanyl residue replacing Glu-98
J. Biol. Chem.
270
15557-15562
1995
Lactobacillus leichmannii
Kaminski, P.A.; Dacher, P.; Dugue, L.; Pochet, S.
In vivo reshaping the catalytic site of nucleoside 2-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution
J. Biol. Chem.
283
20053-20059
2008
Lactobacillus leichmannii (Q9RSV5), Lactobacillus leichmannii, Limosilactobacillus fermentum (Q6YNI5), Limosilactobacillus fermentum, Limosilactobacillus fermentum PAK9 (Q6YNI5)
Kaminski, P.A.; Dugue, L.; Pochet, S.
Expanding substrate specificity of nucleoside 2-deoxyribosyltransferase
Nucleic Acids Symp. Ser.
52
495-496
2008
Lactobacillus leichmannii, Limosilactobacillus fermentum (Q6YNI5)
Kaminski, P.A.; Labesse, G.
Phosphodeoxyribosyltransferases: designed enzymes for deoxyribonucleotide synthesis
J. Biol. Chem.
288
6534-6541
2013
Lactobacillus leichmannii (Q9R5V5)
Fresco-Taboada, A.; de la Mata, I.; Arroyo, M.; Fernandez-Lucas, J.
New insights on nucleoside 2'-deoxyribosyltransferases: a versatile biocatalyst for one-pot one-step synthesis of nucleoside analogs
Appl. Microbiol. Biotechnol.
97
3773-3785
2013
Lactococcus lactis, Lactobacillus leichmannii (Q9R5V5)
Vichier-Guerre, S.; Dugue, L.; Bonhomme, F.; Pochet, S.
Expedient and generic synthesis of imidazole nucleosides by enzymatic transglycosylation
Org. Biomol. Chem.
14
3638-3653
2016
Lactobacillus leichmannii
Del Arco, J.; Perona, A.; Gonzalez, L.; Fernandez-Lucas, J.; Gago, F.; Sanchez-Murcia, P.A.
Reaction mechanism of nucleoside 2-deoxyribosyltransferases free-energy landscape supports an oxocarbenium ion as the reaction intermediate
Org. Biomol. Chem.
17
7891-7899
2019
Lactobacillus leichmannii (Q9R5V5), Lactobacillus leichmannii
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