1YA6

alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a central A:G mismatch

Summary for 1YA6

• Entry DOI: 10.2210/pdb1ya6/pdb
• Related: 1XV5 1Y6F 1Y6G 1Y8Z
• Descriptor: 5'-D(*AP*TP*AP*CP*TP*AP*AP*GP*AP*TP*AP*G)-3', 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*T)-3', DNA alpha-glucosyltransferase, ... (6 entities in total)
• Functional Keywords: glycosyltransferase/dna, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage T4
• Total number of polymer chains: 4
• Total formula weight: 103365.75

Authors

Lariviere, L.,Sommer, N.,Morera, S. (deposition date: 2004-12-17, release date: 2005-08-30, Last modification date: 2023-10-25)

Primary citation

Lariviere, L.,Sommer, N.,Morera, S.
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.
J.Mol.Biol., 352:139-150, 2005

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-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.

PubMed: 16081100
DOI: 10.1016/j.jmb.2005.07.007

Experimental method

X-RAY DIFFRACTION (2.4 Å)