T4 phage BGT in complex with UDP

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 

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This is version 1.3 of the entry. See complete history


High resolution crystal structures of T4 phage beta-glucosyltransferase: induced fit and effect of substrate and metal binding.

Morera, S.Lariviere, L.Kurzeck, J.Aschke-Sonnenborn, U.Freemont, P.S.Janin, J.Ruger, W.

(2001) J Mol Biol 311: 569-577

  • DOI: https://doi.org/10.1006/jmbi.2001.4905
  • Primary Citation of Related Structures:  
    1JEJ, 1JG6, 1JG7, 1JIU, 1JIV, 1JIX

  • PubMed Abstract: 

    beta-Glucosyltransferase (BGT) is a DNA-modifying enzyme encoded by bacteriophage T4 that transfers glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA. We report six X-ray structures of the substrate-free and the UDP-bound enzyme. Four also contain metal ions which activate the enzyme, including Mg(2+) in forms 1 and 2 and Mn(2+) or Ca(2+). The substrate-free BGT structure differs by a domain movement from one previously determined in another space group. Further domain movements are seen in the complex with UDP and the four UDP-metal complexes. Mg(2+), Mn(2+) and Ca(2+) bind near the beta-phosphate of the nucleotide, but they occupy slightly different positions and have different ligands depending on the metal and the crystal form. Whilst the metal site observed in these complexes with the product UDP is not compatible with a role in activating glucose transfer, it approximates the position of the positive charge in the oxocarbonium ion thought to form on the glucose moiety of the substrate during catalysis.

  • Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, UPR 9063 CNRS, Bât.34, 1 Avenue de la Terrasse, Gif-sur-Yvette, 91198, France. morera@lebs.cnrs-gif.fr

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA BETA-GLUCOSYLTRANSFERASE351Tequatrovirus T4Mutation(s): 0 
Find proteins for P04547 (Enterobacteria phage T4)
Explore P04547 
Go to UniProtKB:  P04547
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04547
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UDP

Download Ideal Coordinates CCD File 
C9 H14 N2 O12 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.791α = 90
b = 70.38β = 97.99
c = 59.386γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description