View source for 5bqt


==Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.==
<StructureSection load='5bqt' size='340' side='right'caption='[[5bqt]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5bqt]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BQT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BQT 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]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5bqt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bqt OCA], [https://pdbe.org/5bqt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bqt RCSB], [https://www.ebi.ac.uk/pdbsum/5bqt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bqt ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TMBL2_PYRFU TMBL2_PYRFU] Binds to the maltodextrin transport gene cluster (mdxE operon) promoter and to some other TGM (Thermococcales-Glycolytic-Motif) sequences, but not exclusively.<ref>PMID:17587231</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of TrmBL2 from the archaeon P. furiosus shows an association of two pseudo-symmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix-turn-helix domains binding to successive major grooves of the DNA. However, in TrmBL2 the two dimers are arranged at a mutual displacement of approximately two base pairs so that they associate with the DNA along the double helical axis at an angle of approximately 80 degrees . While the deoxyribose phosphate groups of the dsDNA used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The helix-turn-helix domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent. This hitherto unseen mode of DNA binding by TrmBL2 seem to arise from non-optimal protein-DNA contacts made by its four helix-turn-helix domains resulting in a low-affinity, nonspecific binding to DNA.

Structural insights into nonspecific binding of DNA by TrmBL2, an archaeal chromatin protein.,Ahmad MU, Waege I, Hausner W, Thomm M, Boos W, Diederichs K, Welte W J Mol Biol. 2015 Aug 20. pii: S0022-2836(15)00458-1. doi:, 10.1016/j.jmb.2015.08.012. PMID:26299937<ref>PMID:26299937</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5bqt" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Ahmad MU]]
[[Category: Diederichs K]]
[[Category: Welte W]]