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Information on EC 1.3.1.91 - tRNA-dihydrouridine20 synthase [NAD(P)+]
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1.3.1.91 tRNA-dihydrouridine20 synthase [NAD(P)+]IUBMB Comments
A flavoenzyme . The enzyme specifically modifies uracil20 in tRNA.
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Word Map
- 1.3.1.91
- dsrnas
-
thermus
-
d-loops
- thermophilus
- flavin
- carcinogenesis
-
dsrbd
- archaea
- trnaphe
-
elbow
-
l-shaped
- medicine
- synthase-2
- diagnostics
The enzyme appears in viruses and cellular organisms
Reaction Schemes
5,6-dihydrouracil20 in tRNA
+
=
uracil20 in tRNA
+
+
Synonyms
dihydrouridine synthase, hdus2, dihydrouridine synthase 2, hsdus2, dus 2, dus2p, trna-dihydrouridine synthases, ecodusc, 
more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dihydrouridine synthase
dihydrouridine synthase 2
Dus2p
DusB
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
5,6-dihydrouracil20 in tRNA + NAD(P)+ = uracil20 in tRNA + NAD(P)H + H+
-
-
-
-
5,6-dihydrouracil20 in tRNA + NAD(P)+ = uracil20 in tRNA + NAD(P)H + H+
dsRNA binding mode, modeling
5,6-dihydrouracil20 in tRNA + NAD(P)+ = uracil20 in tRNA + NAD(P)H + H+
Dus proteins adopt a common substrate recognition mechanism using an adapter molecule, whereas the manner of tRNA binding is diverse
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SYSTEMATIC NAME
IUBMB Comments
tRNA-5,6-dihydrouracil20:NAD(P)+ oxidoreductase
A flavoenzyme [3]. The enzyme specifically modifies uracil20 in tRNA.
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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
uracil in bulk tRNA + NADPH + H+
5,6-dihydrouracil in bulk tRNA + NADP+
the enzyme exhibits a clear preference for NADPH compared to NADH
-
-
?
uracil in pre-tRNALeu + NAD(P)H + H+
5,6-dihydrouracil in pre-tRNALeu + NAD(P)+
-
-
-
?
uracil in pre-tRNATyr + NAD(P)H + H+
5,6-dihydrouracil in pre-tRNATyr + NAD(P)+
-
-
-
?
uracil20 in tRNA + NADH + H+
5,6-dihydrouracil20 in tRNA + NAD+
-
-
-
?
uracil20a in tRNA + NADH + H+
5,6-dihydrouracil20a in tRNA + NAD+
-
-
-
?
more the enzyme it is not able to synthetize uracil16 in tRNA
?
-
-
-
?
more the enzyme it is not able to synthetize uracil16 in tRNA
?
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
uracil in bulk tRNA + NADH + H+
5,6-dihydrouracil in bulk tRNA + NAD+
the enzyme exhibits a clear preference for NADPH compared to NADH
-
-
?
uracil in bulk tRNA + NADH + H+
5,6-dihydrouracil in bulk tRNA + NAD+
Mycoplasma capricolum subsp. capricolum ATCC 14323
the enzyme exhibits a clear preference for NADPH compared to NADH
-
-
?
uracil in tRNA + NAD(P)H + H+
5,6-dihydrouracil in tRNA + NAD(P)+
-
-
-
?
uracil in tRNA + NAD(P)H + H+
5,6-dihydrouracil in tRNA + NAD(P)+
the enzyme is specific for the proR hydrogen of NADPH. Cys117 is very important for the reduction of tRNA
-
-
r
uracil17 in tRNA + NADPH + H+
5,6-dihydrouracil17 in tRNA + NADP+
-
-
-
?
uracil17 in tRNA + NADPH + H+
5,6-dihydrouracil17 in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
uracil20 in tRNA + NAD(P)H + H+
5,6-dihydrouracil20 in tRNA + NAD(P)+
-
-
-
?
uracil20 in tRNA + NAD(P)H + H+
5,6-dihydrouracil20 in tRNA + NAD(P)+
the enzyme specifically modifies uracil20 in tRNA, e.g. tRNALeu(CAA) and tRNATyr
-
-
?
uracil20 in tRNA + NAD(P)H + H+
5,6-dihydrouracil20 in tRNA + NAD(P)+
e.g. tRNALeu(CAA) and tRNATyr
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
-
?
uracil20a in tRNA + NADPH + H+
5,6-dihydrouracil20a in tRNA + NADP+
-
-
-
?
uracil20a in tRNA + NADPH + H+
5,6-dihydrouracil20a in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
additional information
?
-
tRNA recognition mechanism, overview
-
-
?
additional information
?
-
no enzymatic activity ith tRNAAsp substrate
-
-
?
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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
uracil in tRNA + NAD(P)H + H+
5,6-dihydrouracil in tRNA + NAD(P)+
-
-
-
?
uracil20 in tRNA + NADH + H+
5,6-dihydrouracil20 in tRNA + NAD+
-
-
-
?
uracil20a in tRNA + NADH + H+
5,6-dihydrouracil20a in tRNA + NAD+
-
-
-
?
uracil17 in tRNA + NADPH + H+
5,6-dihydrouracil17 in tRNA + NADP+
-
-
-
?
uracil17 in tRNA + NADPH + H+
5,6-dihydrouracil17 in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
uracil20 in tRNA + NAD(P)H + H+
5,6-dihydrouracil20 in tRNA + NAD(P)+
-
-
-
?
uracil20 in tRNA + NAD(P)H + H+
5,6-dihydrouracil20 in tRNA + NAD(P)+
the enzyme specifically modifies uracil20 in tRNA, e.g. tRNALeu(CAA) and tRNATyr
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
uracil20 in tRNA + NADPH + H+
5,6-dihydrouracil20 in tRNA + NADP+
-
-
-
-
?
uracil20a in tRNA + NADPH + H+
5,6-dihydrouracil20a in tRNA + NADP+
-
-
-
?
uracil20a in tRNA + NADPH + H+
5,6-dihydrouracil20a in tRNA + NADP+
Mycoplasma capricolum subsp. capricolum ATCC 14323
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FMN
the flavin cofactor is involved in the reduction of uridine, FMN binding site structure, overview. HsDus2dusD binds the FMN cofactor non-covalently at the C-terminal end of the beta-barrel, above beta-strands 1 and 8
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Carcinogenesis
A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis.
Carcinogenesis
Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase.
Carcinogenesis
From bacterial to human dihydrouridine synthase: automated structure determination.
Lung Neoplasms
A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis.
Neoplasms
From bacterial to human dihydrouridine synthase: automated structure determination.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
Michaelis-Menten kinetics
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
kinetics of reductive and oxidative half-reactions
-
additional information
additional information
-
kinetics of reductive and oxidative half-reactions
-
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
overexpression of hDUS2 in nonsmall cell lung carcinomas is identified by analysis of the gene-expression profiles
brenda
elevated hDus2 mRNA and protein levels
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
comparison of structure and substrate recognition mechanisms of Thermus thermophilus Dus and Escherichia coli Dus enzymes, overview
evolution
In humans, there are four Dus enzymes. The hDus2 subfamily is proposed to specifically modify U20. The overall fold of the human Dus2 is similar to that of bacterial enzymes, but has a larger recognition domain and a unique three-stranded antiparallel beta-sheet insertion into the catalytic domain that packs next to the recognition domain, contributing to domain-domain interactions
evolution
while in Dus enzymes from bacteria, plants and fungi, tRNA binding is essentially achieved by the alpha-helical domain, in HsDus2 this function is carried out by the dsRNA binding domain (dsRBD)
malfunction
a small interfering RNA against hDUS2 transfected into NSCLC cells suppresses expression of the gene, reduces the amount of dihydrouridine in tRNA molecules, and suppresses growth
malfunction
yeast extract from a dus1-DELTA strain is completely defective in modification of yeast pre-tRNAPhe
malfunction
increased expression of human dihydrouridine synthase 2 (hDus2) is linked to pulmonary carcinogenesis, while its knockdown decreases cancer cell line viability
physiological function
formation of dihydrouridine in yeast cytoplasmic tRNAs is carried out by a family of four dihydrouridine synthases (Dus1p, Dus2p, Dus3p, and Dus4p), each acting at specific positions in tRNAs. Dus1p modifies U16 and U17, Dus2p modifies U20, Dus3p modifies U47, and Dus4p modifies U20a and U20b. These four proteins are responsible for all dihydrouridine modification of cytoplasmic tRNAs in yeast
physiological function
dihydrouridine is produced by dihydrouridine synthase (Dus) by enzymatic reduction of the C5-C6 bond in uridine
physiological function
in tRNA, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. Formation of dihydrouridine 20, located in the D-loop, is catalyzed by dihydrouridine synthase 2 (Dus2). Full-length HsDus2 but not its Dus domain complements a DELTAdus2 yeast strain by catalyzing formation of dihydrouridine20
additional information
residues that participate in binding to the adapter molecule in EcoDusC are Asn95, Lys139, Arg141, His168 and Arg170. The catalytic cysteine residue is Cys98
additional information
-
residues that participate in binding to the adapter molecule in EcoDusC are Asn95, Lys139, Arg141, His168 and Arg170. The catalytic cysteine residue is Cys98
additional information
the catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRNA binding domain (dsRBD). HsDus2 catalytic domain structure, overview
additional information
-
the catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRNA binding domain (dsRBD). HsDus2 catalytic domain structure, overview
additional information
tRNA binding and the active site structure, overview
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
additional information
the enzyme is composed of two domains: an N-terminal catalytic domain and a C-terminal tRNA-binding domain
additional information
-
the enzyme is composed of two domains: an N-terminal catalytic domain and a C-terminal tRNA-binding domain
additional information
the N-terminal catalytic domain contains the flavin cofactor involved in the reduction of uridine. The second module is the conserved alpha-helical domain known as the tRNA binding domain in HsDus2 homologues. It is connected via a flexible linker to an unusual extended version of a dsRNA binding domain (dsRBD). The catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRBD. Domain architecture of HsDus2, enzyme MALDI peptide mass finger printing analysis, overview
additional information
-
the N-terminal catalytic domain contains the flavin cofactor involved in the reduction of uridine. The second module is the conserved alpha-helical domain known as the tRNA binding domain in HsDus2 homologues. It is connected via a flexible linker to an unusual extended version of a dsRNA binding domain (dsRBD). The catalytic domain binds selectively NADPH but cannot reduce uridine in the absence of the dsRBD. Domain architecture of HsDus2, enzyme MALDI peptide mass finger printing analysis, overview
additional information
three-dimensional structure analysis of wild-type and selenomethionine-labeled hDus2 catalytic and tRNA-recognition domains, and modeling, overview
additional information
-
three-dimensional structure analysis of wild-type and selenomethionine-labeled hDus2 catalytic and tRNA-recognition domains, and modeling, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged and SeMet-labeled DusC, sitting drop vapour diffusion method, mixing of 200 nl of about 10 mg/ml of protein in 20 mM HEPES, pH 7.6, 1 mM MgCl2, 200 mM KCl, 7 mM 2-mercaptoethanol, and 10% glycerol, with 200 nl of reservoir solution containing 0.1 M Tris, pH 7.9, 0.2 M sodium acetate, and 12% PEG 4000 for the wild-type enzyme and 0.1 M imidazole, pH 8.0, 15% v/v 2-propanol, and 20% v/v glycerol for the SeMet-labeled enzyme, X-ray diffraction structure determination and analysis at 2.1 A resolution
vapor diffusion method, using 1.6 M lithium sulfate and 100 mM HEPES pH 7.5
mutant enzyme E294K, vapor diffusion method, using 30% (w/v) PEG 2000 MME, 200 mM ammonium sulfate, and 50 mM sodium acetate pH 5.5. Mutant enzyme E294K/Q305K, vapor diffusion method, using 30% (w/v) PEG 2000 MME, 200 mM ammonium sulfate, and 50 mM sodium acetate pH 5.0. Mutant enzyme Q305K, vapor diffusion method, using 2.2 M ammonium sulfate
purified recombinant catalytic HsDus2dusD domain and tRNA binding domain HsDus2dsRBD (Glu347-Lys451), by hanging drop vapor diffusion method, at 19°C, X-ray diffraction structure determination and crystal structure analysis, PDB IDs 4WFS and 4WFT
purified recombinant hDus2 catalytic and tRNA-recognition domains (residues 1-340), sitting drop vapour diffusion method, 300 nl of 10 mg/ml protein in 20 mM Tris, pH 8.0, 100 mM NaCl, 5 mM imidazole, and 5 mM DTT, are mixed with 0. 54 ml of reservoir solution containing 0.1 M MES-malic acid-Tris, pH 4.0, and 25% w/v PEG 1500, 2 days, 19°C, X-ray diffraction structure determination and analysis by single-wavelength anomalous diffraction at 1.9 A resolution, automated molecular replacement with different search models, and modeling
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E294K
the mutation increases the tRNA binding affinity and dihydrouridine activity compared to the wild type enzyme
E294K/Q305K
the mutation increases the tRNA binding affinity and dihydrouridine activity compared to the wild type enzyme
Q305K
the mutation increases the tRNA binding affinity and dihydrouridine activity compared to the wild type enzyme
C117A
rate constant is 1600fold lower than the rate constant of the wild-type enzyme
additional information
additional information
siRNA-dependent knockdown of hDus2 decreases colony formation and cell viability of non-small cell lung cancer cells, while hDus2 immunohistochemical staining correlated with patient survival
additional information
-
siRNA-dependent knockdown of hDus2 decreases colony formation and cell viability of non-small cell lung cancer cells, while hDus2 immunohistochemical staining correlated with patient survival
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HiTrap column chromatography and Superdex S200 gel filtration
Ni-NTA column chromatography and Superdex S200 gel filtration
recombinant His-tagged enzyme by nickel affinity chromatography and gel filtration
recombinant His-tagged wild-type and selenomethionine-labeled enzymes from Escherichia coli cell-free extract (centrifugation at 40000 x g) by nickel affinity chromatography, dialysis, heparin affinity chromatography, and gel filtration
recombinant wild-type and selenomethionine-labeled hDus2 1-340 fragment, comprising the hDus2 catalytic and tRNA-recognition domains, from Escherichia coli strains BL21(DE3) and B834(DE3), respectively
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21DE3 Star cells
expression in Escherichia coli. There is a higher proportion of tRNAGly in Escherichia coli expressinf DUS2
recombinant expression of His-tagged enzyme as wild-type and selenomethionine-labeled proteins in Escherichia coli strains BL21(DE3) and B834 (DE3), respectively
recombinant expression of His-tagged enzyme, functional complementation of an enzyme-deficient Saccharomyces cerevisiae mutant by expression of enzyme domains HsDus2dusD and HsDus2dsRBD, both domains are required for activity
recombinant expression of wild-type and selenomethionine-labeled hDus2 1-340 fragment, comprising the hDus2 catalytic and tRNA-recognition domains, in Escherichia coli strains BL21(DE3) and B834(DE3), respectively
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
upregulation of hDUS2 is a relatively common feature of pulmonary carcinogenesis
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
diagnostics
the enzyme defined as an independent prognostic factor for the development of non-small cell lung cancer cells
medicine
medicine
upregulation of hDUS2 is a relatively common feature of pulmonary carcinogenesis. Selective suppression of hDUS2 enzyme activity and/or inhibition of formation of the hDUS2-tRNA synthetase complex could be a promising therapeutic strategy for treatment of many lung cancers. Significant association between higher levels of hDUS2 in tumors and poorer prognosis of lung cancer patients
medicine
the enzyme may serve as a valuable target for therapeutic intervention in pulmonary carcinogenesis
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kato, T.; Daigo, Y.; Hayama, S.; Ishikawa, N.; Yamabuki, T.; Ito, T.; Miyamoto, M.; Kondo, S.; Nakamura, Y.
A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis
Cancer Res.
65
5638-5646
2005
Homo sapiens (Q9NX74), Homo sapiens
brenda
Xing, F.; Hiley, S.L.; Hughes, T.R.; Phizicky, E.M.
The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs
J. Biol. Chem.
279
17850-17860
2004
Saccharomyces cerevisiae (P53720), Saccharomyces cerevisiae
brenda
Rider, L.W.; Ottosen, M.B.; Gattis, S.G.; Palfey, B.A.
Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction
J. Biol. Chem.
284
10324-10333
2009
Saccharomyces cerevisiae (P53720), Saccharomyces cerevisiae
brenda
Xing, F.; Martzen, M.R.; Phizicky, E.M.
A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA
RNA
8
370-381
2002
Saccharomyces cerevisiae (P53720), Saccharomyces cerevisiae
brenda
Whelan, F.; Jenkins, H.T.; Griffiths, S.C.; Byrne, R.T.; Dodson, E.J.; Antson, A.A.
From bacterial to human dihydrouridine synthase automated structure determination
Acta Crystallogr. Sect. D
71
1564-1571
2015
Homo sapiens (Q9NX74), Homo sapiens
brenda
Chen, M.; Yu, J.; Tanaka, Y.; Tanaka, M.; Tanaka, I.; Yao, M.
Structure of dihydrouridine synthase C (DusC) from Escherichia coli
Acta Crystallogr. Sect. F
69
834-838
2013
Escherichia coli (P33371), Escherichia coli
brenda
Bou-Nader, C.; Pecqueur, L.; Bregeon, D.; Kamah, A.; Guerineau, V.; Golinelli-Pimpaneau, B.; Guimaraes, B.G.; Fontecave, M.; Hamdane, D.
An extended dsRBD is required for post-transcriptional modification in human tRNAs
Nucleic Acids Res.
43
9446-9456
2015
Homo sapiens (Q9NX74), Homo sapiens
brenda
Bou-Nader, C.; Bregeon, D.; Pecqueur, L.; Fontecave, M.; Hamdane, D.
Electrostatic potential in the tRNA binding evolution of dihydrouridine synthases
Biochemistry
57
5407-5414
2018
Saccharomyces cerevisiae, Homo sapiens (Q9NX74)
brenda
Bou-Nader, C.; Montemont, H.; Guerineau, V.; Jean-Jean, O.; Bregeon, D.; Hamdane, D.
Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases Perspectives on the evolution scenario
Nucleic Acids Res.
46
1386-1394
2018
Escherichia coli (P32695)
brenda
Faivre, B.; Lombard, M.; Fakroun, S.; Vo, C.; Goyenvalle, C.; Guerineau, V.; Pecqueur, L.; Fontecave, M.; De Crecy-Lagard, V.; Bregeon, D.; Hamdane, D.
Dihydrouridine synthesis in tRNAs is under reductive evolution in Mollicutes
RNA Biol.
18
2278-2289
2021
Mycoplasma capricolum subsp. capricolum (A0A084EMY4), Mycoplasma capricolum subsp. capricolum ATCC 14323 (A0A084EMY4)
brenda
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