EzCatDB: D00403

DB codeD00403
RLCP classification3.903.70210.354
CATH domainDomain 13.40.50.2000Catalytic domain
Domain 23.40.50.2000
E.C.2.4.1.27
CSA1c3j


Enzyme Name
Swiss-protKEGG

P04547
Protein nameDNA beta-glucosyltransferaseDNA 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
SynonymsBeta-GT
BGT
EC 2.4.1.27


Swiss-prot:Accession NumberP04547
Entry nameGSTB_BPT4
ActivityTransfers a beta-D-glucosyl residue from UDP- glucose to an hydroxymethylcytosine residue in DNA.
SubunitMonomer.
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00029C03997L00009C00015
CompoundMagnesiumUDP-glucose5-hydroxymethylcytosine in DNAalpha-glucosyl-5-hydroxymethylcytosine in DNAUDP
Typedivalent metal (Ca2+, Mg2+)amide group,carbohydrate,nucleotideamine group,amide group,carbohydrate,nucleic acidsaromatic ring (with nitrogen atoms),carbohydrate,nucleic acidsamide group,nucleotide
1c3jA01UnboundUnboundUnboundUnboundUnbound
1qkjA01UnboundUnboundUnboundUnboundUnbound
2bgtA01UnboundUnboundUnboundUnboundUnbound
2bguA01UnboundUnboundUnboundUnboundUnbound
1ixyA01Bound:_MGUnboundAnalogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G(chain C)UnboundUnbound
1ixyB01Bound:_MGUnboundAnalogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G(chain D)UnboundUnbound
1m5rA01UnboundUnboundAnalogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G(chain C)UnboundUnbound
1m5rB01UnboundUnboundAnalogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G(chain D)UnboundUnbound
1jejA01UnboundUnboundUnboundUnboundUnbound
1jg6A01UnboundUnboundUnboundUnboundUnbound
1jg7A01Analogue:_MNUnboundUnboundUnboundUnbound
1jiuA01Bound:_MGUnboundUnboundUnboundUnbound
1jivA01Bound:2x_MGUnboundUnboundUnboundUnbound
1jixA01Analogue:_CAUnboundUnboundUnboundUnbound
1c3jA02UnboundUnboundUnboundUnboundBound:UDP
1qkjA02UnboundUnboundUnboundUnboundBound:UDP
2bgtA02UnboundUnboundUnboundUnboundUnbound
2bguA02UnboundUnboundUnboundUnboundBound:UDP
1ixyA02UnboundUnboundUnboundUnboundBound:UDP
1ixyB02UnboundUnboundUnboundUnboundBound:UDP
1m5rA02UnboundUnboundUnboundUnboundBound:UDP
1m5rB02UnboundUnboundUnboundUnboundBound:UDP
1jejA02UnboundUnboundUnboundUnboundUnbound
1jg6A02UnboundUnboundUnboundUnboundBound:UDP
1jg7A02UnboundUnboundUnboundUnboundBound:UDP
1jiuA02UnboundUnboundUnboundUnboundBound:UDP
1jivA02UnboundUnboundUnboundUnboundBound:UDP
1jixA02UnboundUnboundUnboundUnboundBound:UDP

Active-site residues
pdbCatalytic residuesCofactor-binding residues
1c3jA01ASP 100
GLU 163(Mg2+ binding)
1qkjA01ASP 100
GLU 163(Mg2+ binding)
2bgtA01ASP 100
GLU 163(Mg2+ binding)
2bguA01ASP 100
GLU 163(Mg2+ binding)
1ixyA01ASP 100
GLU 163(Mg2+ binding)
1ixyB01ASP 100
GLU 163(Mg2+ binding)
1m5rA01ASP 100
GLU 163(Mg2+ binding)
1m5rB01ASP 100
GLU 163(Mg2+ binding)
1jejA01ASP 100
GLU 163(Mg2+ binding)
1jg6A01ASP 100
GLU 163(Mg2+ binding)
1jg7A01ASP 100
GLU 163(Mg2+ binding)
1jiuA01ASP 100
GLU 163(Mg2+ binding)
1jivA01ASP 100
GLU 163(Mg2+ binding)
1jixA01ASP 100
GLU 163(Mg2+ binding)
1c3jA02

1qkjA02

2bgtA02

2bguA02

1ixyA02

1ixyB02

1m5rA02

1m5rB02

1jejA02

1jg6A02

1jg7A02

1jiuA02

1jivA02

1jixA02


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.3418-3420
[2]Fig.5, p.7262
[4]Fig.4, p.487-4882

references
[1]
PubMed ID8062817
JournalEMBO J
Year1994
Volume13
Pages3413-22
AuthorsVrielink A, Ruger W, Driessen HP, Freemont PS
TitleCrystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
Related PDB1bgt,1bgu
Related Swiss-protP04547
[2]
PubMed ID10497034
JournalJ Mol Biol
Year1999
Volume292
Pages717-30
AuthorsMorera S, Imberty A, Aschke-Sonnenborn U, Ruger W, Freemont PS
TitleT4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
Related PDB1c3j,1qkj
Related Swiss-protP04547
[3]
PubMed ID11493010
JournalJ Mol Biol
Year2001
Volume311
Pages569-77
AuthorsMorera S, Lariviere L, Kurzeck J, Aschke-Sonnenborn U, Freemont PS, Janin J, Ruger W
TitleHigh resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.
Related PDB1jej,1jg6,1jg7,1jiu,1jiv,1jix
[4]
PubMed ID12445783
JournalJ Mol Biol
Year2002
Volume324
Pages483-90
AuthorsLariviere L, Morera S
TitleA base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.
Related PDB1ixy,1m5r

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).

createdupdated
2002-05-012011-09-28
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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