4xqw: Difference between revisions
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==X-ray structure analysis of xylanase-N44E with MES at pH6.0== | ==X-ray structure analysis of xylanase-N44E with MES at pH6.0== | ||
<StructureSection load='4xqw' size='340' side='right' caption='[[4xqw]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='4xqw' size='340' side='right'caption='[[4xqw]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4xqw]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4xqw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichoderma_reesei Trichoderma reesei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XQW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XQW FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xqw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xqw OCA], [https://pdbe.org/4xqw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xqw RCSB], [https://www.ebi.ac.uk/pdbsum/4xqw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xqw ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/XYN2_HYPJR XYN2_HYPJR] Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).<ref>PMID:1369024</ref> <ref>PMID:19556747</ref> <ref>PMID:7988708</ref> <ref>PMID:1369024</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 23: | Line 23: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Trichoderma reesei]] | ||
[[Category: Coates | [[Category: Coates L]] | ||
[[Category: Fisher | [[Category: Fisher Z]] | ||
[[Category: Graham | [[Category: Graham DE]] | ||
[[Category: Hanson | [[Category: Hanson LB]] | ||
[[Category: Kovalevsky | [[Category: Kovalevsky AY]] | ||
[[Category: Langan | [[Category: Langan P]] | ||
[[Category: Ostermann | [[Category: Ostermann A]] | ||
[[Category: Park | [[Category: Park JM]] | ||
[[Category: Riccardi | [[Category: Riccardi DM]] | ||
[[Category: Schrader | [[Category: Schrader T]] | ||
[[Category: Smith | [[Category: Smith JC]] | ||
[[Category: Wan | [[Category: Wan Q]] | ||
Latest revision as of 10:48, 27 September 2023
X-ray structure analysis of xylanase-N44E with MES at pH6.0X-ray structure analysis of xylanase-N44E with MES at pH6.0
Structural highlights
FunctionXYN2_HYPJR Glycoside hydrolase involved in the hydrolysis of xylan, a major plant cell wall hemicellulose made up of 1,4-beta-linked D-xylopyranose residues. Catalyzes the endohydrolysis of the main-chain 1,4-beta-glycosidic bonds connecting the xylose subunits yielding various xylooligosaccharides and xylose (PubMed:1369024, Ref.5). The catalysis proceeds by a double-displacement reaction mechanism with a putative covalent glycosyl-enzyme intermediate, with retention of the anomeric configuration (PubMed:7988708). Produces xylobiose and xylose as the main degradation products (PubMed:19556747).[1] [2] [3] [4] Publication Abstract from PubMedGlycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.,Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A Proc Natl Acad Sci U S A. 2015 Sep 21. pii: 201504986. PMID:26392527[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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