D00403
type: Enzyme
rlcp: p354
cath: Rossmann fold
ec: https://purl.uniprot.org/enzyme/2.4.1.27
csa: 1c3j
uniprot: P04547
kegg enzyme: DNA beta-glucosyltransferase
kegg enzyme: T4-HMC-beta-glucosyl transferase
kegg enzyme: T4-beta-glucosyl transferase
kegg enzyme: T4 phage beta-glucosyltransferase
kegg enzyme: UDP glucose-DNA beta-glucosyltransferase
kegg enzyme: uridine diphosphoglucose-deoxyribonucleate beta-glucosyltransferase
kegg cofactor: Magnesium
kegg substrate: UDP-glucose
kegg substrate: 5-hydroxymethylcytosine in DNA
kegg product: alpha-glucosyl-5-hydroxymethylcytosine in DNA
kegg product: UDP
pdb: 1c3jA01
pdb: 1qkjA01
pdb: 2bgtA01
pdb: 2bguA01
pdb: 1ixyA01
pdb: 1ixyB01
pdb: 1m5rA01
pdb: 1m5rB01
pdb: 1jejA01
pdb: 1jg6A01
pdb: 1jg7A01
pdb: 1jiuA01
pdb: 1jivA01
pdb: 1jixA01
pdb: 1c3jA02
pdb: 1qkjA02
pdb: 2bgtA02
pdb: 2bguA02
pdb: 1ixyA02
pdb: 1ixyB02
pdb: 1m5rA02
pdb: 1m5rB02
pdb: 1jejA02
pdb: 1jg6A02
pdb: 1jg7A02
pdb: 1jiuA02
pdb: 1jivA02
pdb: 1jixA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1c3jA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1qkjA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 2bgtA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 2bguA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1ixyA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1ixyB01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1m5rA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1m5rB01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jejA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jg6A01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jg7A01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jiuA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jivA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jixA01
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1c3jA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1qkjA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 2bgtA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 2bguA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1ixyA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1ixyB02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1m5rA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1m5rB02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jejA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jg6A02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jg7A02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jiuA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jivA02
pdb bound state: Unbound
  compound: UDP-glucose
  pdb: 1jixA02
pdb bound state: Unbound
  compound: 5-hydroxymethylcytosine in DNA
  pdb: 1c3jA01
pdb bound state: Unbound
  compound: 5-hydroxymethylcytosine in DNA
  pdb: 1qkjA01
references: Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
references: T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
references: High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.
references: A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.
comment: 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).

Rossmann fold
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.40.50.2000
catalytic domain: index.html

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

UDP-glucose
type: KeggSubstrate
references: KEGG:C00029
compound type: amide group
compound type: carbohydrate
compound type: nucleotide
references: CHEBI:46229
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

5-hydroxymethylcytosine in DNA
type: KeggSubstrate
references: KEGG:C03997
compound type: amine group
compound type: amide group
compound type: carbohydrate
compound type: nucleic acids
references: CHEBI:16952
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

alpha-glucosyl-5-hydroxymethylcytosine in DNA
type: KeggProduct
references: KEGG:L00009
compound type: aromatic ring (with nitrogen atoms)
compound type: carbohydrate
compound type: nucleic acids

UDP
type: KeggProduct
references: KEGG:C00015
compound type: amide group
compound type: nucleotide
references: CHEBI:17659
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1c3jA01
type: Pdb
references: 1c3j
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1c3j
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1qkjA01
type: Pdb
references: 1qkj
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qkj
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

2bgtA01
type: Pdb
references: 2bgt
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2bgt
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

2bguA01
type: Pdb
references: 2bgu
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2bgu
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1ixyA01
type: Pdb
references: 1ixy
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ixy
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1ixyB01
type: Pdb
references: 1ixy
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ixy
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1m5rA01
type: Pdb
references: 1m5r
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1m5r
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1m5rB01
type: Pdb
references: 1m5r
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1m5r
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jejA01
type: Pdb
references: 1jej
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jej
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jg6A01
type: Pdb
references: 1jg6
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jg6
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jg7A01
type: Pdb
references: 1jg7
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jg7
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jiuA01
type: Pdb
references: 1jiu
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jiu
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jivA01
type: Pdb
references: 1jiv
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jiv
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

1jixA01
type: Pdb
references: 1jix
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1jix
catalytic residue: ASP 100
cofactor binding residue: GLU 163(Mg2+ binding)

Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8062817
journal: EMBO J
volume: 13
pages: 3413-22
published year: 1994
authors:
  item: Vrielink A
  item: Ruger W
  item: Driessen HP
  item: Freemont PS
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P04547

T4 phage beta-glucosyltransferase: substrate binding and proposed catalytic mechanism.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10497034
journal: J Mol Biol
volume: 292
pages: 717-30
published year: 1999
authors:
  item: Morera S
  item: Imberty A
  item: Aschke-Sonnenborn U
  item: Ruger W
  item: Freemont PS
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P04547

High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11493010
journal: J Mol Biol
volume: 311
pages: 569-77
published year: 2001
authors:
  item: Morera S
  item: Lariviere L
  item: Kurzeck J
  item: Aschke-Sonnenborn U
  item: Freemont PS
  item: Janin J
  item: Ruger W
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12445783
journal: J Mol Biol
volume: 324
pages: 483-90
published year: 2002
authors:
  item: Lariviere L
  item: Morera S
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Analogue
compound: 5-hydroxymethylcytosine in DNA
pdb: 1ixyA01
ligand het code: G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C)

Analogue
compound: 5-hydroxymethylcytosine in DNA
pdb: 1ixyB01
ligand het code: G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D)

Analogue
compound: 5-hydroxymethylcytosine in DNA
pdb: 1m5rA01
ligand het code: G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain C)

Analogue
compound: 5-hydroxymethylcytosine in DNA
pdb: 1m5rB01
ligand het code: G-A-T-A-C-T-3DR-A-G-A-T-A-G (chain D)

Analogue
compound: Magnesium
pdb: 1jg7A01
ligand het code: _MN

Analogue
compound: Magnesium
pdb: 1jixA01
ligand het code: _CA

ReferenceForCatalyticMechanism
reference index: 1
reference section: p.3418-3420

ReferenceForCatalyticMechanism
reference index: 2
reference section: Fig.5, p.726
reference step: 2

ReferenceForCatalyticMechanism
reference index: 4
reference section: Fig.4, p.487-488
reference step: 2