1Y6F

alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  1XV5, 1Y6G, 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA alpha-glucosyltransferase
A, B
403Enterobacteria phage T4Gene Names: agt
EC: 2.4.1.26
Find proteins for P04519 (Enterobacteria phage T4)
Go to UniProtKB:  P04519
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'C13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'D13N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UPG
Query on UPG

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-GLUCOSE
URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-JZMIEXBBSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

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

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
C
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.363α = 90.00
b = 123.964β = 101.83
c = 86.628γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance