DB code: D00403

RLCP classification	3.903.70210.354 : Transfer
CATH domain	3.40.50.2000 : Rossmann fold	Catalytic domain
CATH 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 18420	46229 46229	16952 16952		17659 17659
PubChem	888 888	8629 8629	440189 440189		6031 6031

1c3jA01	Unbound	Unbound	Unbound	Unbound	Unbound
1qkjA01	Unbound	Unbound	Unbound	Unbound	Unbound
2bgtA01	Unbound	Unbound	Unbound	Unbound	Unbound
2bguA01	Unbound	Unbound	Unbound	Unbound	Unbound
1ixyA01	Bound:_MG	Unbound	Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C)	Unbound	Unbound
1ixyB01	Bound:_MG	Unbound	Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D)	Unbound	Unbound
1m5rA01	Unbound	Unbound	Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C)	Unbound	Unbound
1m5rB01	Unbound	Unbound	Analogue:G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D)	Unbound	Unbound
1jejA01	Unbound	Unbound	Unbound	Unbound	Unbound
1jg6A01	Unbound	Unbound	Unbound	Unbound	Unbound
1jg7A01	Analogue:_MN	Unbound	Unbound	Unbound	Unbound
1jiuA01	Bound:_MG	Unbound	Unbound	Unbound	Unbound
1jivA01	Bound:2x_MG	Unbound	Unbound	Unbound	Unbound
1jixA01	Analogue:_CA	Unbound	Unbound	Unbound	Unbound
1c3jA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1qkjA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
2bgtA02	Unbound	Unbound	Unbound	Unbound	Unbound
2bguA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1ixyA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1ixyB02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1m5rA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1m5rB02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1jejA02	Unbound	Unbound	Unbound	Unbound	Unbound
1jg6A02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1jg7A02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1jiuA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1jivA02	Unbound	Unbound	Unbound	Unbound	Bound:UDP
1jixA02	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	ASP 100	GLU 163(Mg2+ binding)
1qkjA01	ASP 100	GLU 163(Mg2+ binding)
2bgtA01	ASP 100	GLU 163(Mg2+ binding)
2bguA01	ASP 100	GLU 163(Mg2+ binding)
1ixyA01	ASP 100	GLU 163(Mg2+ binding)
1ixyB01	ASP 100	GLU 163(Mg2+ binding)
1m5rA01	ASP 100	GLU 163(Mg2+ binding)
1m5rB01	ASP 100	GLU 163(Mg2+ binding)
1jejA01	ASP 100	GLU 163(Mg2+ binding)
1jg6A01	ASP 100	GLU 163(Mg2+ binding)
1jg7A01	ASP 100	GLU 163(Mg2+ binding)
1jiuA01	ASP 100	GLU 163(Mg2+ binding)
1jivA01	ASP 100	GLU 163(Mg2+ binding)
1jixA01	ASP 100	GLU 163(Mg2+ binding)
1c3jA02
1qkjA02
2bgtA02
2bguA02
1ixyA02
1ixyB02
1m5rA02
1m5rB02
1jejA02
1jg6A02
1jg7A02
1jiuA02
1jivA02
1jixA02

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).

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