1Y8Z

alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.

Lariviere, L.Sommer, N.Morera, S.

(2005) J Mol Biol 352: 139-150

  • DOI: 10.1016/j.jmb.2005.07.007
  • Primary Citation of Related Structures:  
    1Y6G, 1Y6F, 1XV5, 1Y8Z, 1YA6

  • PubMed Abstract: 
  • The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5- ...

    The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form an alpha-glucosidic linkage and a beta-glucosidic linkage, respectively. Five structures of AGT have been determined: a binary complex with the UDP product and four ternary complexes with UDP or UDP-glucose and oligonucleotides containing an A:G, HMU:G (hydroxymethyl uracyl) or AP:G (apurinic/apyrimidinic) mismatch at the target base-pair. AGT adopts the GT-B fold, one of the two folds known for GTs. However, while the sugar donor binding mode is classical for a GT-B enzyme, the sugar acceptor binding mode is unexpected and breaks the established consensus: AGT is the first GT-B enzyme that predominantly binds both the sugar donor and acceptor to the C-terminal domain. Its active site pocket is highly similar to four retaining GT-B glycosyltransferases (trehalose-6-phosphate synthase, glycogen synthase, glycogen and maltodextrin phosphorylases) strongly suggesting a common evolutionary origin and catalytic mechanism for these enzymes. Structure-guided mutagenesis and kinetic analysis do not permit identification of a nucleophile residue responsible for a glycosyl-enzyme intermediate for the classical double displacement mechanism. Interestingly, the DNA structures reveal partially flipped-out bases. They provide evidence for a passive role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA alpha-glucosyltransferaseAB402Escherichia virus T4Mutation(s): 2 
Gene Names: agt
EC: 2.4.1.26
Find proteins for P04519 (Enterobacteria phage T4)
Explore P04519 
Go to UniProtKB:  P04519
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*(5HU)P*AP*GP*AP*TP*AP*G)-3'C13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*G)-3'D9N/A
      Small Molecules
      Ligands 4 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
      NCO
      Query on NCO

      Download CCD File 
      A, B, D
      COBALT HEXAMMINE(III)
      Co H18 N6
      DYLMFCCYOUSRTK-FGTKAUEHAT
       Ligand Interaction
      GOL
      Query on GOL

      Download CCD File 
      A, B
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

      Download CCD File 
      B
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      CME
      Query on CME
      A,BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.90 Å
      • R-Value Free: 0.250 
      • R-Value Work: 0.208 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 41.263α = 90
      b = 114.655β = 89.49
      c = 86.143γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing
      CNSrefinement

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2005-08-30
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Non-polymer description, Version format compliance
      • Version 1.3: 2020-07-22
        Changes: Advisory, Database references, Derived calculations