1ixy: Difference between revisions
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New page: left|200px<br /><applet load="1ixy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ixy, resolution 2.5Å" /> '''Ternary complex of T4... |
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== | ==Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex== | ||
T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized | <StructureSection load='1ixy' size='340' side='right'caption='[[1ixy]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ixy]] is a 6 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=1IXY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXY FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></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=1ixy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixy OCA], [https://pdbe.org/1ixy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixy RCSB], [https://www.ebi.ac.uk/pdbsum/1ixy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixy ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/GSTB_BPT4 GSTB_BPT4] Catalyzes the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. 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;"> | |||
== Publication Abstract from PubMed == | |||
T4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. Both structures reveal a large distortion in the bound DNA. BGT flips the deoxyribose moiety at the abasic site to an extra-helical position and induces a 40 degrees bend in the DNA with a marked widening of the major groove. The Tris molecule mimics the glucose moiety in its transition state. The base-flipping mechanism, which has so far been observed only for glycosylases, methyltransferases and endonucleases, is now reported for a glucosyltransferase. BGT is unique in binding and inserting a loop into the DNA duplex through the major groove only. Furthermore, BGT compresses the backbone DNA one base further than the target base on the 3'-side. | |||
A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.,Lariviere L, Morera S J Mol Biol. 2002 Nov 29;324(3):483-90. PMID:12445783<ref>PMID:12445783</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1ixy" style="background-color:#fffaf0;"></div> | ||
== References == | |||
[[Category: | <references/> | ||
[[Category: Lariviere | __TOC__ | ||
[[Category: Morera | </StructureSection> | ||
[[Category: Escherichia virus T4]] | |||
[[Category: Large Structures]] | |||
[[Category: Lariviere L]] | |||
[[Category: Morera S]] | |||
Latest revision as of 11:36, 16 August 2023
Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplexTernary complex of T4 phage BGT with UDP and a 13 mer DNA duplex
Structural highlights
FunctionGSTB_BPT4 Catalyzes the transfer of glucose (Glc) from uridine diphosphoglucose (UDP-Glc) to 5-hydroxymethylcytosine (5-HMC) in double-stranded DNA. 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 PubMedT4 phage beta-glucosyltransferase (BGT) modifies T4 DNA. We crystallized BGT with UDP-glucose and a 13mer DNA fragment containing an abasic site. We obtained two crystal structures of a ternary complex BGT-UDP-DNA at 1.8A and 2.5A resolution, one with a Tris molecule and the other with a metal ion at the active site. Both structures reveal a large distortion in the bound DNA. BGT flips the deoxyribose moiety at the abasic site to an extra-helical position and induces a 40 degrees bend in the DNA with a marked widening of the major groove. The Tris molecule mimics the glucose moiety in its transition state. The base-flipping mechanism, which has so far been observed only for glycosylases, methyltransferases and endonucleases, is now reported for a glucosyltransferase. BGT is unique in binding and inserting a loop into the DNA duplex through the major groove only. Furthermore, BGT compresses the backbone DNA one base further than the target base on the 3'-side. A base-flipping mechanism for the T4 phage beta-glucosyltransferase and identification of a transition-state analog.,Lariviere L, Morera S J Mol Biol. 2002 Nov 29;324(3):483-90. PMID:12445783[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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