1BGU

CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSFERASE IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE DIPHOSPHOGLUCOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.

Vrielink, A.Ruger, W.Driessen, H.P.Freemont, P.S.

(1994) EMBO J. 13: 3413-3422

  • Primary Citation of Related Structures:  1BGT, 2BGT, 2BGU
  • Also Cited By: 1QKJ

  • PubMed Abstract: 
  • Bacteriophage T4 beta-glucosyltransferase (EC 2.4.1.27) catalyses the transfer of glucose from uridine diphosphoglucose to hydroxymethyl groups of modified cytosine bases in T4 duplex DNA forming beta-glycosidic linkages. The enzyme forms part of a p ...

    Bacteriophage T4 beta-glucosyltransferase (EC 2.4.1.27) catalyses the transfer of glucose from uridine diphosphoglucose to hydroxymethyl groups of modified cytosine bases in T4 duplex DNA forming beta-glycosidic linkages. The enzyme forms part of a phage DNA protection system. We have solved and refined the crystal structure of recombinant beta-glucosyltransferase to 2.2 A resolution in the presence and absence of the substrate, uridine diphosphoglucose. The structure comprises two domains of similar topology, each reminiscent of a nucleotide binding fold. The two domains are separated by a central cleft which generates a concave surface along one side of the molecule. The substrate-bound complex reveals only clear electron density for the uridine diphosphate portion of the substrate. The UDPG is bound in a pocket at the bottom of the cleft between the two domains and makes extensive hydrogen bonding contacts with residues of the C-terminal domain only. The domains undergo a rigid body conformational change causing the structure to adopt a more closed conformation upon ligand binding. The movement of the domains is facilitated by a hinge region between residues 166 and 172. Electrostatic surface potential calculations reveal a large positive potential along the concave surface of the structure, suggesting a possible site for duplex DNA interaction.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Studies of T4 Phage Beta-Glucosyltransferase
      Freemont, P.S.,Rueger, W.
      (1988) J.Mol.Biol. 203: 525
    • T4-Induced Alpha-and Beta-Glucosyltransferase: Cloning of the Genes and a Comparison of Their Products Based on Sequencing Data
      Tomaschewski, J.,Gram, H.,Crabb, J.W.,Ruger, W.
      (1985) Nucleic Acids Res. 13: 7551


    Organizational Affiliation

    Protein Structure Laboratory, Imperial Cancer Research Fund, London.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-GLUCOSYLTRANSFERASE
A
351Enterobacteria phage T4Gene Names: bgt
EC: 2.4.1.27
Find proteins for P04547 (Enterobacteria phage T4)
Go to UniProtKB:  P04547
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 151.920α = 90.00
b = 52.260β = 90.00
c = 52.740γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other