1m5r: Difference between revisions

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New page: left|200px<br /><applet load="1m5r" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m5r, resolution 1.8Å" /> '''Ternary complex of T4...
 
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[[Image:1m5r.gif|left|200px]]<br /><applet load="1m5r" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1m5r, resolution 1.8&Aring;" />
'''Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex'''<br />


==Overview==
==Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex==
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.
<StructureSection load='1m5r' size='340' side='right'caption='[[1m5r]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
1M5R 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 UDP, TRS and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M5R 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]] 1.8&#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=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>
==Reference==
<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>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12445783 12445783]
</table>
[[Category: Bacteriophage t4]]
== Function ==
[[Category: DNA beta-glucosyltransferase]]
[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.
[[Category: Single protein]]
__TOC__
[[Category: Lariviere, L.]]
</StructureSection>
[[Category: Morera, S.]]
[[Category: Escherichia virus T4]]
[[Category: MPD]]
[[Category: Large Structures]]
[[Category: TRS]]
[[Category: Lariviere L]]
[[Category: UDP]]
[[Category: Morera S]]
[[Category: abasic site]]
[[Category: base-flipping]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:10:03 2007''

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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