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1y6f

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[[Image:1y6f.gif|left|200px]]<br /><applet load="1y6f" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1y6f.gif|left|200px]]
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caption="1y6f, resolution 2.4&Aring;" />
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'''alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site'''<br />
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{{Structure
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|PDB= 1y6f |SIZE=350|CAPTION= <scene name='initialview01'>1y6f</scene>, resolution 2.4&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=UPG:URIDINE-5'-DIPHOSPHATE-GLUCOSE'>UPG</scene>, <scene name='pdbligand=UDP:URIDINE-5'-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> and <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>
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|ACTIVITY= [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]
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|GENE=
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}}
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'''alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1Y6F 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].
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1Y6F is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6F OCA].
==Reference==
==Reference==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16081100 16081100]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/16081100 16081100]
[[Category: Bacteriophage t4]]
[[Category: Bacteriophage t4]]
[[Category: DNA alpha-glucosyltransferase]]
[[Category: DNA alpha-glucosyltransferase]]
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[[Category: transferase]]
[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:16 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:18:58 2008''

Revision as of 13:18, 20 March 2008

Image:1y6f.gif


PDB ID 1y6f

Drag the structure with the mouse to rotate
, resolution 2.4Å
Ligands: , , and
Activity: DNA alpha-glucosyltransferase, with EC number 2.4.1.26
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 Bacteriophage 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

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