1SXQ | pdb_00001sxq

BGT in complex with a 13mer DNA containing a central C:G base pair and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structural evidence of a passive base flipping mechanism for {beta}-Glucosyltransferase

Lariviere, L.Morera, S.

(2004) J Biological Chem 279: 34715-34720

  • DOI: https://doi.org/10.1074/jbc.M404394200
  • Primary Citation of Related Structures:  
    1SXP, 1SXQ

  • PubMed Abstract: 

    Beta-glucosyltransferase (BGT) is a DNA-modifying enzyme and a glycosyltransferase. This inverting enzyme transfers glucose from UDP-glucose to the 5-hydroxymethyl cytosine bases of T4 phage DNA. From previous structural analyses we showed that Asp-100 and Asn-70 were, respectively, the catalytic base and the key residue for specific DNA recognition (Larivière, L., Gueguen-Chaignon, V., and Moréra, S. (2003) J. Mol. Biol. 330, 1077-1086). Here, we supply biochemical evidence supporting their essential roles in catalysis. We have also shown previously that BGT uses a base-flipping mechanism to access 5-hydroxymethyl cytosine (Larivière, L., and Moréra, S. (2002) J. Mol. Biol. 324, 483-490). Whether it is an active or a passive process remains unclear, as is the case for all DNA cleaving and modifying enzymes. Here, we report two crystal structures: (i) BGT in complex with a 13-mer DNA containing an A:G mismatch and (ii) BGT in a ternary complex with UDP and an oligonucleotide containing a single central G:C base pair. The binary structure reveals a specific complex with the flipped-out, mismatched adenine exposed to the active site. Unexpectedly, the other structure shows the non-productive binding of an intermediate flipped-out base. Our structural analysis provides clear evidence for a passive process.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Unité Propre de Recherche 9063 CNRS, Bātiment 34, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA beta-glucosyltransferaseE [auth A],
F [auth B]
351Tequatrovirus T4Mutation(s): 0 
Gene Names: BGTBETA-GT
EC: 2.4.1.27
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.652α = 90
b = 70.157β = 90.55
c = 96.581γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations