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| | <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 [https://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 [https://proteopedia.org/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" id="ligandDat"><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"><div style='overflow: auto; max-height: 3em;'>[[1xv5|1xv5]], [[1y6g|1y6g]], [[1y8z|1y8z]], [[1ya6|1ya6]]</div></td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA_alpha-glucosyltransferase DNA alpha-glucosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.26 2.4.1.26] </span></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='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> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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.
| + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpt4]] | + | [[Category: Escherichia virus T4]] |
| - | [[Category: DNA alpha-glucosyltransferase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lariviere, L]] | + | [[Category: Lariviere L]] |
| - | [[Category: Morera, S]] | + | [[Category: Morera S]] |
| - | [[Category: Sommer, N]] | + | [[Category: Sommer N]] |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
1y6f is a 4 chain structure with sequence from Escherichia virus T4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.4Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
GSTA_BPT4 Is involved in a DNA modification process to protect the phage genome against its own nucleases and the host restriction endonuclease system.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lariviere L, Sommer N, Morera S. Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase. J Mol Biol. 2005 Sep 9;352(1):139-50. PMID:16081100 doi:S0022-2836(05)00784-9
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