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| ==alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site== | | ==alpha-glucosyltransferase in complex with UDP-glucose and DNA containing an abasic site== |
| <StructureSection load='1y6f' size='340' side='right' caption='[[1y6f]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='1y6f' size='340' side='right'caption='[[1y6f]], [[Resolution|resolution]] 2.40Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[1y6f]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y6F FirstGlance]. <br> | | <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> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></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> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1xv5|1xv5]], [[1y6g|1y6g]], [[1y8z|1y8z]], [[1ya6|1ya6]]</td></tr> | | <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> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
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| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y6f OCA], [http://pdbe.org/1y6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y6f RCSB], [http://www.ebi.ac.uk/pdbsum/1y6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y6f ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://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. | | [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. |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| 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.
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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:16081100<ref>PMID:16081100</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 1y6f" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Bpt4]] | | [[Category: Escherichia virus T4]] |
| [[Category: DNA alpha-glucosyltransferase]] | | [[Category: Large Structures]] |
| [[Category: Lariviere, L]] | | [[Category: Lariviere L]] |
| [[Category: Morera, S]] | | [[Category: Morera S]] |
| [[Category: Sommer, N]] | | [[Category: Sommer N]] |
| [[Category: Transferase]]
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| [[Category: Transferase-dna complex]]
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