2exh: Difference between revisions

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<StructureSection load='2exh' size='340' side='right'caption='[[2exh]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
<StructureSection load='2exh' size='340' side='right'caption='[[2exh]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2exh]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXH FirstGlance]. <br>
<table><tr><td colspan='2'>[[2exh]] 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=2EXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EXH FirstGlance]. <br>
</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></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.88&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2exi|2exi]], [[2exj|2exj]], [[2exk|2exk]]</div></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></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></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=2exh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exh OCA], [https://pdbe.org/2exh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exh RCSB], [https://www.ebi.ac.uk/pdbsum/2exh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exh ProSAT]</span></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=2exh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2exh OCA], [https://pdbe.org/2exh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2exh RCSB], [https://www.ebi.ac.uk/pdbsum/2exh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2exh ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q09LX0_GEOSE Q09LX0_GEOSE]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2exh ConSurf].
</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=2exh ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:16631196<ref>PMID:16631196</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2exh" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
*[[Xylosidase 3D structures|Xylosidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 12980]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Large Structures]]
[[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: Yuval S]]
[[Category: Yuval, S]]
[[Category: Family43]]
[[Category: Glykosidase]]
[[Category: Hydrolase]]
[[Category: Hydrolsase]]
[[Category: Xylosidase]]

Latest revision as of 12:20, 14 February 2024

Structure of the family43 beta-Xylosidase from geobacillus stearothermophilusStructure of the family43 beta-Xylosidase from geobacillus stearothermophilus

Structural highlights

2exh 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 1.88Å
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

2exh, resolution 1.88Å

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