Information on EC 2.4.1.27 - DNA beta-glucosyltransferase

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The expected taxonomic range for this enzyme is: Enterobacteria phage T4

EC NUMBER
COMMENTARY hide
2.4.1.27
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RECOMMENDED NAME
GeneOntology No.
DNA beta-glucosyltransferase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Transfers a beta-D-glucosyl residue from UDP-glucose to an hydroxymethylcytosine residue in DNA
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexosyl group transfer
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-
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SYSTEMATIC NAME
IUBMB Comments
UDP-glucose:DNA beta-D-glucosyltransferase
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CAS REGISTRY NUMBER
COMMENTARY hide
9030-14-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
UDP-D-glucose + 5-hydroxymethyl cytosine
UDP + 5-hydroxymethyl cytosine beta-D-glucoside
show the reaction diagram
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5-hydroxymethyl cytosine residues of duplex DNA
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-
?
UDP-D-glucose + 5-hydroxymethyl cytosine containing DNA
UDP + 5-hydroxymethyl cytosine beta-D-glucoside containing DNA
show the reaction diagram
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recombinant enzyme glucosylates 5-hydroxymethyl cytosine containing DNA in a nonprocessive manner, and binding to either 5-hydroxymethyl cytosine containing DNA or uridine diphosphoglucose substrates is random, with both binary complexes being catalytically competent. The numbers of 5-hydroxymethyl cytosine on target sequences influence the turnover numbers for the recombinant enzyme
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?
UDP-D-glucose + 5-hydroxymethyl cytosine containing phage T4 DNA
UDP + 5-hydroxymethyl cytosine beta-D-glucoside containing phage T4 DNA
show the reaction diagram
-
-
-
-
?
UDP-D-glucose + DNA containing 12 5-hydroxymethyl cytosine residues
UDP + ?
show the reaction diagram
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-
-
-
?
UDP-D-glucose + DNA containing 2 5-hydroxymethyl cytosine residues
UDP + ?
show the reaction diagram
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-
-
-
?
UDP-D-glucose + DNA containing 24 5-hydroxymethyl cytosine residues
UDP + ?
show the reaction diagram
-
-
-
-
?
UDP-D-glucose + DNA containing 6 5-hydroxymethyl cytosine residues
UDP + ?
show the reaction diagram
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-
-
-
?
UDPglucose + 5-hydroxymethylcytosine containing DNA
UDP + beta-glucosyl-5-hydroxymethylcytosine containing DNA
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
UDP-D-glucose + 5-hydroxymethyl cytosine
UDP + 5-hydroxymethyl cytosine beta-D-glucoside
show the reaction diagram
-
5-hydroxymethyl cytosine residues of duplex DNA
-
-
?
UDPglucose + 5-hydroxymethylcytosine containing DNA
UDP + beta-glucosyl-5-hydroxymethylcytosine containing DNA
show the reaction diagram
additional information
?
-
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the AGT with GT-B glycosyltransferase fold is responsible for DNA base flipping and substrate recognition, mechanism, overview
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
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four of the six X-ray structures of the enzyme contain metal ions which activate the enzyme, including Mg2+ in forms 1 and 2 and Mn2+ or Ca2+. Mg2+, Mn2+ and Ca2+ bind near the beta-phosphate of the nucleotide, but they occupy slightly different positions
Mg2+
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four of the six X-ray structures of the enzyme contain metal ions which activate the enzyme, including Mg2+ in forms 1 and 2 and Mn2+ or Ca2+. Mg2+, Mn2+ and Ca2+ bind near the beta-phosphate of the nucleotide, but they occupy slightly different positions
Mn2+
-
four of the six X-ray structures of the enzyme contain metal ions which activate the enzyme, including Mg2+ in forms 1 and 2 and Mn2+ or Ca2+. Mg2+, Mn2+ and Ca2+ bind near the beta-phosphate of the nucleotide, but they occupy slightly different positions
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5-hydroxymethyl cytosine beta-D-glucoside containing DNA
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competitive inhibitor with respect to 5-hydroxymethyl cytosine containing DNA and mixed inhibitor with respect to UDP-glucose
UDP
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competitive inhibitor with respect to UDP-glucose and mixed inhibitor with respect to 5-hydroxymethyl cytosine containing DNA
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0004
5-hydroxymethyl cytosine containing phage T4 DNA
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pH 7.9, 25C
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0.00023
DNA containing 12 5-hydroxymethyl cytosine residues
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pH 7.9, 25C
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0.003
DNA containing 2 5-hydroxymethyl cytosine residues
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pH 7.9, 25C
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0.00022
DNA containing 24 5-hydroxymethyl cytosine residues
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pH 7.9, 25C
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0.0006
DNA containing 6 5-hydroxymethyl cytosine residues
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pH 7.9, 25C
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0.016
UDP-D-glucose
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pH 7.9, 25C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.283
5-hydroxymethyl cytosine containing phage T4 DNA
Enterobacteria phage T4
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pH 7.9, 25C
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1.033
DNA containing 12 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
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2.8
DNA containing 2 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
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9.66
DNA containing 24 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
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1.666
DNA containing 6 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3200
5-hydroxymethyl cytosine containing phage T4 DNA
Enterobacteria phage T4
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pH 7.9, 25C
42202
4483
DNA containing 12 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
42205
933
DNA containing 2 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
42203
4400
DNA containing 24 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
42206
2766
DNA containing 6 5-hydroxymethyl cytosine residues
Enterobacteria phage T4
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pH 7.9, 25C
42204
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.003 - 0.004
5-hydroxymethyl cytosine beta-D-glucoside containing DNA
0.002 - 0.009
UDP
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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structural analysis of domain folding, substrate binding, catalytic mechanism, and base flipping mechanism, overview
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of the recombinant enzyme in the presence and absence of the substrate, UDPglucose; ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site
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crystallization of the enzyme with UDPglucose and a 13mer DNA fragment containing an abasic site. Two crystal structures are obtained of a ternary complex BGT-UDP-DNA at 1.8 A and 2.5 A resolution, one with a Tris molecule and the other with a metal ion at the active site; ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site
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ternary complex between the T4 phage beta-glucosyltransferase, uridine diphosphoglucose and a DNA fragment containing an abasic site
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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use of recombinant enzyme to estimate global 5-hydroxymethyl cytosine content in a variety of genomic DNAs. Most of the genomic DNAs derived from vertebrate tissue and cell lines contain 5-hydroxymethyl cytosine. DNA from mouse, human, and bovine brains displays 0.5?0.9% of the total nucleotides as 5-hydroxymethyl cytosine, which is higher compared to the levels found in other tissues. A comparison between cancer and healthy tissue genomes suggests a lower percentage of 5-hydroxymethyl cytosine in cancer
medicine
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a comparison between cancer and healthy tissue genomes suggests a lower percentage of 5-hydroxymethyl cytosine in cancer