1m5r: Difference between revisions

Revision as of 14:51, 21 February 2008

Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex

OverviewOverview

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.

About this StructureAbout this Structure

1M5R is a Single protein structure of sequence from Bacteriophage t4 with , and as ligands. Active as DNA beta-glucosyltransferase, with EC number 2.4.1.27 Full crystallographic information is available from OCA.

ReferenceReference

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

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-[[Image:1m5r.gif|left|200px]]<br /><applet load="1m5r" size="450" color="white" frame="true" align="right" spinBox="true"
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 '''Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-M5R 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].
+M5R 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 <scene name='pdbligand=UDP:'>UDP</scene>, <scene name='pdbligand=TRS:'>TRS</scene> and <scene name='pdbligand=MPD:'>MPD</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5R OCA].
 ==Reference==
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 [[Category: protein-dna complex]]
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