2vrq: Difference between revisions
New page: '''Unreleased structure''' The entry 2vrq is ON HOLD until Paper Publication Authors: Paes, G., Skov, L.K., ODonohue, M.J., Remond, C., Kastrup, J.S., Gajhede, M., Mirza, O. Descriptio... |
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==STRUCTURE OF AN INACTIVE MUTANT OF ARABINOFURANOSIDASE FROM THERMOBACILLUS XYLANILYTICUS IN COMPLEX WITH A PENTASACCHARIDE== | |||
<StructureSection load='2vrq' size='340' side='right'caption='[[2vrq]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2vrq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobacillus_xylanilyticus Thermobacillus xylanilyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VRQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VRQ 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]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</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=2vrq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vrq OCA], [https://pdbe.org/2vrq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vrq RCSB], [https://www.ebi.ac.uk/pdbsum/2vrq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vrq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/O69262_THEXY O69262_THEXY] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vr/2vrq_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vrq ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of the family GH-51 alpha- l-arabinofuranosidase from Thermobacillus xylanilyticus has been solved as a seleno-methionyl derivative. In addition, the structure of an inactive mutant Glu176Gln is presented in complex with a branched pentasaccharide, a fragment of its natural substrate xylan. The overall structure shows the two characteristic GH-51 domains: a catalytic domain that is folded into a (beta/alpha) 8-barrel and a C-terminal domain that displays jelly roll architecture. The pentasaccharide is bound in a groove on the surface of the enzyme, with the mono arabinosyl branch entering a tight pocket harboring the catalytic dyad. Detailed analyses of both structures and comparisons with the two previously determined structures from Geobacillus stearothermophilus and Clostridium thermocellum reveal important details unique to the Thermobacillus xylanilyticus enzyme. In the absence of substrate, the enzyme adopts an open conformation. In the substrate-bound form, the long loop connecting beta-strand 2 to alpha-helix 2 closes the active site and interacts with the substrate through residues His98 and Trp99. The results of kinetic and fluorescence titration studies using mutants underline the importance of this loop, and support the notion of an interaction between Trp99 and the bound substrate. We suggest that the changes in loop conformation are an integral part of the T. xylanilyticus alpha- l-arabinofuranosidase reaction mechanism, and ensure efficient binding and release of substrate. | |||
The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit.,Paes G, Skov LK, O'Donohue MJ, Remond C, Kastrup JS, Gajhede M, Mirza O Biochemistry. 2008 Jul 15;47(28):7441-51. Epub 2008 Jun 19. PMID:18563919<ref>PMID:18563919</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vrq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermobacillus xylanilyticus]] | |||
[[Category: Gajhede M]] | |||
[[Category: Kastrup JS]] | |||
[[Category: Mirza O]] | |||
[[Category: Odonohue MJ]] | |||
[[Category: Paes G]] | |||
[[Category: Remond C]] | |||
[[Category: Skov LK]] | |||