1y6g
From Proteopedia
(New page: 200px<br /><applet load="1y6g" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y6g, resolution 2.8Å" /> '''alpha-glucosyltransfe...) |
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| - | [[Image:1y6g.gif|left|200px]]<br /><applet load="1y6g" size=" | + | [[Image:1y6g.gif|left|200px]]<br /><applet load="1y6g" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1y6g, resolution 2.8Å" /> | caption="1y6g, resolution 2.8Å" /> | ||
'''alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution'''<br /> | '''alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The Escherichia coli T4 bacteriophage uses two glycosyltransferases to | + | 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== | ==About this Structure== | ||
| - | 1Y6G 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 CL, NCO, UDP and EDO 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:// | + | 1Y6G 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=CL:'>CL</scene>, <scene name='pdbligand=NCO:'>NCO</scene>, <scene name='pdbligand=UDP:'>UDP</scene> and <scene name='pdbligand=EDO:'>EDO</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=1Y6G OCA]. |
==Reference== | ==Reference== | ||
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[[Category: transferase]] | [[Category: transferase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:11 2008'' |
Revision as of 14:02, 21 February 2008
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alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution
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
1Y6G 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.
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 Thu Feb 21 16:02:11 2008
Categories: Bacteriophage t4 | DNA alpha-glucosyltransferase | Single protein | Lariviere, L. | Morera, S. | Sommer, N. | CL | EDO | NCO | UDP | Transferase
