BRENDA - Enzyme Database
show all sequences of 2.1.2.8

Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex

Song, H.K.; Sohn, S.H.; Suh, S.W.; EMBO J. 18, 1104-1113 (1999)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene 42 encoding enzyme is sequenced and expressed in Escherichia coli
Escherichia virus T4
Crystallization (Commentary)
Crystallization
Organism
crystal structure in the presence of substrate dCMP at 1.6 A resolution
Escherichia virus T4
Engineering
Amino acid exchange
Commentary
Organism
D179N
mutant with altered substrate preference, favoring dUMP rather than dCMP
Escherichia virus T4
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
28450
-
2 * 28450, homodimer of 246-residue subunits
Escherichia virus T4
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
enzyme forms part of phage DNA protection system
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
5-hydroxymethyl-dCMP is essential for DNA synthesis in phage T4
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
involved in biosynthesis of DNA precursor
Escherichia virus T4
?
additional information
Escherichia virus T4
enzyme functions in vivo as a component of a multienzyme complex called dNTP synthetase
?
-
-
-
additional information
Escherichia virus T4
enzyme is part of a complex efficiently channeling DNA precursors to the replication apparatus
?
-
-
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia virus T4
P08773
-
-
Purification (Commentary)
Commentary
Organism
purification of His6-tagged enzyme
Escherichia virus T4
Reaction
Reaction
Commentary
Organism
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate = tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
catalytic mechanism
Escherichia virus T4
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
enzyme forms part of phage DNA protection system
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
5-hydroxymethyl-dCMP is essential for DNA synthesis in phage T4
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
involved in biosynthesis of DNA precursor
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
enzyme structure, dCMP binding site, folate cofactor binding site, way of substrate binding in the active site, key catalytic residue Cys-148 acts as nucleophile to attack the C6-atom of the cytosine base
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
-
485792
Escherichia virus T4
?
additional information
enzyme functions in vivo as a component of a multienzyme complex called dNTP synthetase
485792
Escherichia virus T4
?
-
-
-
-
additional information
enzyme is part of a complex efficiently channeling DNA precursors to the replication apparatus
485792
Escherichia virus T4
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
homodimer
2 * 28450, homodimer of 246-residue subunits
Escherichia virus T4
Cofactor
Cofactor
Commentary
Organism
Structure
5,10-methylenetetrahydrofolate
as cofactor; weak binding of the folate cofactor to enzyme
Escherichia virus T4
tetrahydrofolate
-
Escherichia virus T4
Cloned(Commentary) (protein specific)
Commentary
Organism
gene 42 encoding enzyme is sequenced and expressed in Escherichia coli
Escherichia virus T4
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
5,10-methylenetetrahydrofolate
as cofactor; weak binding of the folate cofactor to enzyme
Escherichia virus T4
tetrahydrofolate
-
Escherichia virus T4
Crystallization (Commentary) (protein specific)
Crystallization
Organism
crystal structure in the presence of substrate dCMP at 1.6 A resolution
Escherichia virus T4
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D179N
mutant with altered substrate preference, favoring dUMP rather than dCMP
Escherichia virus T4
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
28450
-
2 * 28450, homodimer of 246-residue subunits
Escherichia virus T4
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
enzyme forms part of phage DNA protection system
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
5-hydroxymethyl-dCMP is essential for DNA synthesis in phage T4
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
Escherichia virus T4
-
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
involved in biosynthesis of DNA precursor
Escherichia virus T4
?
additional information
Escherichia virus T4
enzyme functions in vivo as a component of a multienzyme complex called dNTP synthetase
?
-
-
-
additional information
Escherichia virus T4
enzyme is part of a complex efficiently channeling DNA precursors to the replication apparatus
?
-
-
-
Purification (Commentary) (protein specific)
Commentary
Organism
purification of His6-tagged enzyme
Escherichia virus T4
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
enzyme forms part of phage DNA protection system
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
5-hydroxymethyl-dCMP is essential for DNA synthesis in phage T4
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
-
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
involved in biosynthesis of DNA precursor
485792
Escherichia virus T4
?
5,10-methylenetetrahydrofolate + H2O + deoxycytidylate
enzyme structure, dCMP binding site, folate cofactor binding site, way of substrate binding in the active site, key catalytic residue Cys-148 acts as nucleophile to attack the C6-atom of the cytosine base
485792
Escherichia virus T4
tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
-
485792
Escherichia virus T4
?
additional information
enzyme functions in vivo as a component of a multienzyme complex called dNTP synthetase
485792
Escherichia virus T4
?
-
-
-
-
additional information
enzyme is part of a complex efficiently channeling DNA precursors to the replication apparatus
485792
Escherichia virus T4
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
2 * 28450, homodimer of 246-residue subunits
Escherichia virus T4
Other publictions for EC 2.1.2.8
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
735967
Chen
-
Evidence from 18O feeding stud ...
T4virus
Chin. Sci. Bull.
58
864-868
2013
-
-
-
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-
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-
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-
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-
1
-
1
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3
-
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-
1
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1
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1
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-
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-
3
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
659367
Shen
Escherichia coli nucleoside di ...
Escherichia coli
J. Biol. Chem.
279
32225-32232
2004
-
-
-
-
-
-
-
-
-
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1
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3
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1
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1
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1
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-
485792
Song
Crystal structure of deoxycyti ...
Escherichia virus T4
EMBO J.
18
1104-1113
1999
-
-
1
1
1
-
-
-
-
-
1
5
-
2
-
-
1
1
-
-
-
-
6
1
-
-
-
-
-
-
-
2
-
-
-
-
-
1
2
1
1
-
-
-
-
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1
5
-
-
-
1
-
-
-
-
6
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
485791
Hardy
Electrostatic guidance of cata ...
Escherichia virus T4
Biochemistry
34
8422-8432
1995
-
-
1
-
2
-
2
-
-
-
1
1
-
3
-
-
1
1
-
-
-
-
2
1
-
-
-
3
-
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-
2
1
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1
2
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2
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2
1
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1
1
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1
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2
1
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-
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3
-
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-
-
-
485789
Graves
Kinetic and equilibrium alpha- ...
Escherichia virus T4
Biochemistry
33
13049-13056
1994
-
-
1
-
3
-
1
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-
1
1
-
2
-
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1
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2
1
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2
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1
2
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3
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-
1
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1
1
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-
-
-
2
1
-
-
-
-
-
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-
-
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-
485790
Butler
Evidence from 18O exchange stu ...
Escherichia virus T4
Biochemistry
33
10521-10526
1994
-
-
1
-
2
-
4
-
-
-
-
1
-
2
-
-
-
1
-
-
2
-
3
1
-
-
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2
3
-
-
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-
1
2
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2
-
-
4
3
-
-
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-
1
-
-
-
-
-
-
2
-
3
1
-
-
-
-
-
-
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-
-
-
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-
-
485788
Mathews
Enzyme interactions involving ...
Escherichia virus T4
Adv. Exp. Med. Biol.
338
563-570
1993
-
-
1
-
1
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-
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-
-
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2
-
1
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3
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2
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1
2
-
1
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2
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3
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485787
Subramaniam
On the inhibition of deoxycyti ...
Escherichia virus T4
Arch. Biochem. Biophys.
275
11-15
1989
-
-
-
-
-
-
1
1
-
-
-
1
-
1
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-
1
1
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1
-
2
-
1
-
-
-
-
-
-
2
1
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-
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-
2
-
-
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-
1
1
1
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1
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1
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1
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2
-
1
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485783
Lamm
Deoxycytidylate hydroxymethyla ...
Enterobacteria phage T2, Enterobacteria phage T6, Escherichia virus T4
Eur. J. Biochem.
172
553-563
1988
-
-
3
-
1
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4
-
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5
-
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2
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1
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3
1
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1
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6
-
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3
6
-
1
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-
4
-
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2
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1
-
3
1
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1
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-
-
485785
Lee
Deoxycytidylate hydroxymethyla ...
Escherichia virus T4
Biochemistry
27
1367-1373
1988
1
-
-
-
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-
5
1
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-
2
-
-
2
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1
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-
1
2
1
1
1
-
1
-
1
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2
3
-
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1
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2
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5
3
1
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-
2
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1
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1
2
1
1
1
-
1
-
1
-
-
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-
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-
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-
-
485782
Lamm
Nucleotide sequence of the deo ...
Escherichia virus T4
Nucleic Acids Res.
15
3920
1987
-
-
1
-
-
-
-
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-
1
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-
2
-
-
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1
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1
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1
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209854
Allen
T4 phage deoxyribonucleotide-s ...
Escherichia virus T4
J. Biol. Chem.
258
5746-5753
1983
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-
1
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2
2
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1
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3
1
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2
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3
1
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485786
North
T4 phage-coded deoxycytidylate ...
Escherichia virus T4
Biochem. Biophys. Res. Commun.
77
898-904
1977
-
-
1
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1
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3
2
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1
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1
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1
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1
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1
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2
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1
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1
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3
1
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485780
Mathews
Virus-induced acquisition of m ...
bacteriophage T6r+
J. Biol. Chem.
239
2957-2963
1964
-
-
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1
1
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1
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1
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1
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1
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1
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1
1
2
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1
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485781
Pizer
Virus-induced acquisition of m ...
bacteriophage T6r+
J. Biol. Chem.
237
1251-1259
1962
-
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1
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