2exk: Difference between revisions

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New page: left|200px<br /><applet load="2exk" size="350" color="white" frame="true" align="right" spinBox="true" caption="2exk, resolution 2.200Å" /> '''Structure of the fa...
 
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[[Image:2exk.gif|left|200px]]<br /><applet load="2exk" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2exk, resolution 2.200&Aring;" />
'''Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose'''<br />


==Overview==
==Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose==
beta-D-Xylosidases are glycoside hydrolases that catalyze the release of, xylose units from short xylooligosaccharides and are engaged in the final, breakdown of plant cell-wall hemicellulose. Here we describe the, enzyme-substrate crystal structure of an inverting family 43, beta-xylosidase, from Geobacillus stearothermophilus T-6 (XynB3). Each, XynB3 monomeric subunit is organized in two domains: an N-terminal, five-bladed beta-propeller catalytic domain, and a beta-sandwich domain., The active site possesses a pocket topology, which is mainly constructed, from the beta-propeller domain residues, and is closed on one side by a, loop that originates from the beta-sandwich domain. This loop restricts, the length of xylose units that can enter the active site, consistent with, the exo mode of action of the enzyme. Structures of the enzyme-substrate, (xylobiose) complex provide insights into the role of the three catalytic, residues. The xylose moiety at the -1 subsite is held by a large number of, hydrogen bonds, whereas only one hydroxyl of the xylose unit at the +1, subsite can create hydrogen bonds with the enzyme. The general base, Asp15, is located on the alpha-side of the -1 xylose sugar ring, 5.2, Angstroms from the anomeric carbon. This location enables it to activate a, water molecule for a single-displacement attack on the anomeric carbon, resulting in inversion of the anomeric configuration. Glu187, the general, acid, is 2.4 Angstroms from the glycosidic oxygen atom and can protonate, the leaving aglycon. The third catalytic carboxylic acid, Asp128, is 4, Angstroms from the general acid; modulating its pK(a) and keeping it in, the correct orientation relative to the substrate. In addition, Asp128, plays an important role in substrate binding via the 2-O of the glycon, which is important for the transition-state stabilization. Taken together, these key roles explain why Asp128 is an invariant among all five-bladed, beta-propeller glycoside hydrolases.
<StructureSection load='2exk' size='340' side='right'caption='[[2exk]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2exk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXK 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]] 2.2&#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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=2exk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exk OCA], [https://pdbe.org/2exk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exk RCSB], [https://www.ebi.ac.uk/pdbsum/2exk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q09LX0_GEOSE Q09LX0_GEOSE]
== 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/ex/2exk_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2exk ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2EXK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=MES:'>MES</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXK OCA].
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues., Brux C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D, J Mol Biol. 2006 May 26;359(1):97-109. Epub 2006 Mar 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16631196 16631196]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Xylan 1,4-beta-xylosidase]]
[[Category: Brux C]]
[[Category: Brux, C.]]
[[Category: Niefind K]]
[[Category: Niefind, K.]]
[[Category: Schomburg D]]
[[Category: Schomburg, D.]]
[[Category: Shallom-Shezifi D]]
[[Category: Shallom-Shezifi, D.]]
[[Category: Shoham Y]]
[[Category: Shoham, Y.]]
[[Category: CA]]
[[Category: GOL]]
[[Category: MES]]
[[Category: family43]]
[[Category: glykosidase]]
[[Category: hydrolsase]]
[[Category: xylose]]
[[Category: xylosidase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:24:11 2008''

Latest revision as of 12:20, 14 February 2024

Structure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobioseStructure of the family43 beta-Xylosidase E187G from geobacillus stearothermophilus in complex with xylobiose

Structural highlights

2exk is a 4 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q09LX0_GEOSE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2exk, resolution 2.20Å

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