This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1y6f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:37, 13 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[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==
+
==alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site==
-
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.
+
<StructureSection load='1y6f' size='340' side='right'caption='[[1y6f]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1y6f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y6F FirstGlance]. <br>
-
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].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6f OCA], [https://pdbe.org/1y6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y6f RCSB], [https://www.ebi.ac.uk/pdbsum/1y6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6f ProSAT]</span></td></tr>
-
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]
+
</table>
-
[[Category: Bacteriophage t4]]
+
== Function ==
-
[[Category: DNA alpha-glucosyltransferase]]
+
[https://www.uniprot.org/uniprot/GSTA_BPT4 GSTA_BPT4] Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
-
[[Category: Single protein]]
+
__TOC__
-
[[Category: Lariviere, L.]]
+
</StructureSection>
-
[[Category: Morera, S.]]
+
[[Category: Escherichia virus T4]]
-
[[Category: Sommer, N.]]
+
[[Category: Large Structures]]
-
[[Category: GOL]]
+
[[Category: Lariviere L]]
-
[[Category: PEG]]
+
[[Category: Morera S]]
-
[[Category: UDP]]
+
[[Category: Sommer N]]
-
[[Category: UPG]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:16 2008''
+

Current revision

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

PDB ID 1y6f

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y6f"
Personal tools