DB code: D00403

RLCP classification 3.903.70210.354 : Transfer
CATH domain 3.40.50.2000 : Rossmann fold Catalytic domain
3.40.50.2000 : Rossmann fold
E.C. 2.4.1.27
CSA 1c3j
M-CSA 1c3j
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy Pfam
P04547 DNA beta-glucosyltransferase
Beta-GT
BGT
EC 2.4.1.27
NP_049658.1 (Protein)
NC_000866.4 (DNA/RNA sequence)
GT63 (Glycosyltransferase Family 63)
PF09198 (T4-Gluco-transf)
[Graphical View]

KEGG enzyme name
DNA beta-glucosyltransferase
T4-HMC-beta-glucosyl transferase
T4-beta-glucosyl transferase
T4 phage beta-glucosyltransferase
UDP glucose-DNA beta-glucosyltransferase
uridine diphosphoglucose-deoxyribonucleate beta-glucosyltransferase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P04547 GSTB_BPT4 Transfers a beta-D-glucosyl residue from UDP- glucose to an hydroxymethylcytosine residue in DNA. Monomer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00029 C03997 L00009 C00015
E.C.
Compound Magnesium UDP-glucose 5-hydroxymethylcytosine in DNA alpha-glucosyl-5-hydroxymethylcytosine in DNA UDP
Type divalent metal (Ca2+, Mg2+) amide group,carbohydrate,nucleotide amine group,amide group,carbohydrate,nucleic acids aromatic ring (with nitrogen atoms),carbohydrate,nucleic acids amide group,nucleotide
ChEBI 18420
46229
16952
17659
PubChem 888
8629
440189
6031
1c3jA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1qkjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2bgtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2bguA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ixyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C) Unbound Unbound
1ixyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D) Unbound Unbound
1m5rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C) Unbound Unbound
1m5rB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D) Unbound Unbound
1jejA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jg6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jg7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_MN Unbound Unbound Unbound Unbound
1jiuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Unbound
1jivA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound
1jixA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_CA Unbound Unbound Unbound Unbound
1c3jA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1qkjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
2bgtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2bguA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1ixyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1ixyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1m5rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1m5rB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1jejA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1jg6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1jg7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1jiuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1jivA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP
1jixA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:UDP

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c3jA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1qkjA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
2bgtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
2bguA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1ixyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1ixyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1m5rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1m5rB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jejA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jg6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jg7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jiuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jivA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1jixA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 100 GLU 163(Mg2+ binding)
1c3jA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1qkjA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2bgtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2bguA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ixyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ixyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m5rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1m5rB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jejA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jg6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jg7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jiuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jivA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1jixA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
p.3418-3420
[2]
Fig.5, p.726 2
[4]
Fig.4, p.487-488 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 8062817
Journal EMBO J
Year 1994
Volume 13
Pages 3413-22
Authors Vrielink A, Ruger W, Driessen HP, Freemont PS
Title Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
Related PDB 1bgt 1bgu
Related UniProtKB P04547
[2]
Resource
Comments
Medline ID
PubMed ID 10497034
Journal J Mol Biol
Year 1999
Volume 292
Pages 717-30
Authors Morera S, Imberty A, Aschke-Sonnenborn U, Ruger W, Freemont PS
Title T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
Related PDB 1c3j 1qkj
Related UniProtKB P04547
[3]
Resource
Comments
Medline ID
PubMed ID 11493010
Journal J Mol Biol
Year 2001
Volume 311
Pages 569-77
Authors Morera S, Lariviere L, Kurzeck J, Aschke-Sonnenborn U, Freemont PS, Janin J, Ruger W
Title High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.
Related PDB 1jej 1jg6 1jg7 1jiu 1jiv 1jix
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 12445783
Journal J Mol Biol
Year 2002
Volume 324
Pages 483-90
Authors Lariviere L, Morera S
Title A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.
Related PDB 1ixy 1m5r
Related UniProtKB

Comments
This enzyme belongs to glycosyltransferase family-63 (GT63 family), with GT-B fold.
Accoriding to the paper [4], the catalytic mechanism of this enzyme has been proposed as follows:
(1) Asp100 acts as a general base, which abstracts a proton from the acceptor group, hydroxymethyl group, of the 5-HMC base.
(2) This activated acceptor then makes a nucleophilic attack on the C1 atom of glucose in UDP-glucose.
(3) Glucose transfer proceeds via an oxocarbonium ion in its transition state and an inversion of configuration, resulting in the beta-glucosidic linkage.
Moreover, the paper [4] suggested that the geometry of the active site is appropriate for an SN2 direct displacement mechanism.
As for a role of magnesium, although magnesium is necessary for its full activity, there is some controversy, according to the paper [2]. This cationic ion might stablize the transition state, or activate the acceptor group of the substrate, UDP-glucose, together with Asp100. However, according to the crystal structure of this enzyme (PDB 1ixy), the magnesium ion seems to be far away from the site, although it is close to the beta-phosphate of UDP. Thus, it might stabilize the leaving group (donor group).

Created Updated
2002-05-01 2011-09-28