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[[Image:1m5r.gif|left|200px]]


{{Structure
==Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex==
|PDB= 1m5r |SIZE=350|CAPTION= <scene name='initialview01'>1m5r</scene>, resolution 1.8&Aring;
<StructureSection load='1m5r' size='340' side='right'caption='[[1m5r]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=3DR:1&#39;,2&#39;-DIDEOXYRIBOFURANOSE-5&#39;-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UDP:URIDINE-5&#39;-DIPHOSPHATE'>UDP</scene>
<table><tr><td colspan='2'>[[1m5r]] 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=1M5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5R FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_beta-glucosyltransferase DNA beta-glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.27 2.4.1.27] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
|GENE= BGT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])
<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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5r OCA], [https://pdbe.org/1m5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5r RCSB], [https://www.ebi.ac.uk/pdbsum/1m5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5r ProSAT]</span></td></tr>
|RELATEDENTRY=[[1jg6|1JG6]], [[1ixy|1IXY]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5r OCA], [http://www.ebi.ac.uk/pdbsum/1m5r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m5r RCSB]</span>
== 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.
 
__TOC__
'''Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex'''
</StructureSection>
 
[[Category: Escherichia virus T4]]
 
[[Category: Large Structures]]
==Overview==
[[Category: Lariviere L]]
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.
[[Category: Morera S]]
 
==About this Structure==
1M5R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5R OCA].
 
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/12445783 12445783]
[[Category: DNA beta-glucosyltransferase]]
[[Category: Enterobacteria phage t4]]
[[Category: Single protein]]
[[Category: Lariviere, L.]]
[[Category: Morera, S.]]
[[Category: abasic site]]
[[Category: base-flipping]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:11:38 2008''

Latest revision as of 10:40, 14 February 2024

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

1m5r is a 6 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 1.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

1m5r, resolution 1.80Å

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OCA
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