1y6g

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
[[Image:1y6g.gif|left|200px]]<br /><applet load="1y6g" size="350" color="white" frame="true" align="right" spinBox="true"
+
[[Image:1y6g.gif|left|200px]]
-
caption="1y6g, resolution 2.8&Aring;" />
+
 
-
'''alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution'''<br />
+
{{Structure
 +
|PDB= 1y6g |SIZE=350|CAPTION= <scene name='initialview01'>1y6g</scene>, resolution 2.8&Aring;
 +
|SITE=
 +
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=UDP:URIDINE-5'-DIPHOSPHATE'>UDP</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
 +
|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]
 +
|GENE=
 +
}}
 +
 
 +
'''alpha-glucosyltransferase in complex with UDP and a 13_mer DNA containing a HMU base at 2.8 A resolution'''
 +
 
==Overview==
==Overview==
Line 7: Line 16:
==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 <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].
+
1Y6G 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=1Y6G OCA].
==Reference==
==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16081100 16081100]
+
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]]
Line 23: Line 32:
[[Category: transferase]]
[[Category: transferase]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:11 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:18:57 2008''

Revision as of 13:18, 20 March 2008

Image:1y6g.gif


PDB ID 1y6g

Drag the structure with the mouse to rotate
, resolution 2.8Å
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 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. 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 Mar 20 15:18:57 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y6g"
Personal tools