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1y6f
From Proteopedia
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| , resolution 2.4Å | |||||||
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| Ligands: | , , , , , , , , | ||||||
| Activity: | DNA alpha-glucosyltransferase, with EC number 2.4.1.26 | ||||||
| Related: | 1XV5, 1Y6G, 1Y8Z, 1YA6
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site
Overview
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.
About this Structure
1Y6F is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.
Reference
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase., Lariviere L, Sommer N, Morera S, J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:16081100
Page seeded by OCA on Mon Mar 31 00:59:20 2008
