1y6f: Difference between revisions

Revision as of 17:02, 21 February 2008

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

OverviewOverview

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 StructureAbout this Structure

1Y6F is a Single protein structure of sequence from Bacteriophage t4 with , , and as ligands. Active as DNA alpha-glucosyltransferase, with EC number 2.4.1.26 Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:1y6f.gif|left|200px]]<br /><applet load="1y6f" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1y6f.gif|left|200px]]<br /><applet load="1y6f" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1y6f, resolution 2.4&Aring;" />
 '''alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site'''<br />
 ==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.
+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==
-Y6F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with UPG, UDP, GOL and PEG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Y6F OCA].
+Y6F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4] with <scene name='pdbligand=UPG:'>UPG</scene>, <scene name='pdbligand=UDP:'>UDP</scene>, <scene name='pdbligand=GOL:'>GOL</scene> and <scene name='pdbligand=PEG:'>PEG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6F OCA].
 ==Reference==
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 [[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:36:05 2007''
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