1IXY

Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Base-flipping Mechanism for the T4 Phage beta-Glucosyltransferase and Identification of a Transition-state Analog

Lariviere, L.Morera, S.

(2002) J Mol Biol 324: 483-490

  • DOI: 10.1016/s0022-2836(02)01091-4
  • Primary Citation of Related Structures:  
    1M5R, 1IXY

  • PubMed Abstract: 
  • T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one wit ...

    T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. Both structures reveal a large distortion in the bound DNA. BGT flips the deoxyribose moiety at the abasic site to an extra-helical position and induces a 40 degrees bend in the DNA with a marked widening of the major groove. The Tris molecule mimics the glucose moiety in its transition state. The base-flipping mechanism, which has so far been observed only for glycosylases, methyltransferases and endonucleases, is now reported for a glucosyltransferase. BGT is unique in binding and inserting a loop into the DNA duplex through the major groove only. Furthermore, BGT compresses the backbone DNA one base further than the target base on the 3'-side.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA beta-glucosyltransferaseAB351Escherichia virus T4Mutation(s): 0 
Gene Names: bgt
EC: 2.4.1.27
Find proteins for P04547 (Enterobacteria phage T4)
Explore P04547 
Go to UniProtKB:  P04547
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3'C, D13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'E, F13N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      UDP
      Query on UDP

      Download CCD File 
      A, B
      URIDINE-5'-DIPHOSPHATE
      C9 H14 N2 O12 P2
      XCCTYIAWTASOJW-XVFCMESISA-N
       Ligand Interaction
      MPD
      Query on MPD

      Download CCD File 
      A, B
      (4S)-2-METHYL-2,4-PENTANEDIOL
      C6 H14 O2
      SVTBMSDMJJWYQN-YFKPBYRVSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A, B
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.282 
      • R-Value Work: 0.209 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 78.9α = 90
      b = 56.4β = 90.3
      c = 99.1γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALAdata scaling
      AMoREphasing
      CNSrefinement
      CCP4data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-12-04
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance