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| | ==Crystal structure of reducing-end-xylose releasing exo-oligoxylanase Y198F mutant== | | ==Crystal structure of reducing-end-xylose releasing exo-oligoxylanase Y198F mutant== |
| - | <StructureSection load='3a3v' size='340' side='right' caption='[[3a3v]], [[Resolution|resolution]] 1.39Å' scene=''> | + | <StructureSection load='3a3v' size='340' side='right'caption='[[3a3v]], [[Resolution|resolution]] 1.39Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3a3v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_alcalophilus_subsp._halodurans"_boyer_et_al._1973 "bacillus alcalophilus subsp. halodurans" boyer et al. 1973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3A3V FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3a3v]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A3V FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 1.39Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BH2105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 "Bacillus alcalophilus subsp. halodurans" Boyer et al. 1973])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oligosaccharide_reducing-end_xylanase Oligosaccharide reducing-end xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.156 3.2.1.156] </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=3a3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3v OCA], [https://pdbe.org/3a3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a3v RCSB], [https://www.ebi.ac.uk/pdbsum/3a3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3v ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3a3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3v OCA], [http://pdbe.org/3a3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3a3v RCSB], [http://www.ebi.ac.uk/pdbsum/3a3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3v ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/REOX_BACHD REOX_BACHD]] Hydrolyzes xylooligosaccharides with a degree of polymerization of greater than or equal to 3, releasing xylose from the reducing end. Only hydrolyzes the beta anomers of xylooligosaccharides, with inversion of anomeric configuration. Hydrolyzes the glucose and xylose-based trisaccharides where xylose is located at the -1 subsite, GXX, XXG and GXG. Does not hydrolyze xylan, chitosan, lichenan, curdlan or carboxymethylcellulose.<ref>PMID:15491996</ref> | + | [https://www.uniprot.org/uniprot/REOX_HALH5 REOX_HALH5] Hydrolyzes xylooligosaccharides with a degree of polymerization of greater than or equal to 3, releasing xylose from the reducing end. Only hydrolyzes the beta anomers of xylooligosaccharides, with inversion of anomeric configuration. Hydrolyzes the glucose and xylose-based trisaccharides where xylose is located at the -1 subsite, GXX, XXG and GXG. Does not hydrolyze xylan, chitosan, lichenan, curdlan or carboxymethylcellulose.<ref>PMID:15491996</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/3a3v_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/3a3v_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus alcalophilus subsp. halodurans boyer et al. 1973]] | + | [[Category: Alkalihalobacillus halodurans]] |
| - | [[Category: Oligosaccharide reducing-end xylanase]] | + | [[Category: Large Structures]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Hidaka, M]] | + | [[Category: Hidaka M]] |
| - | [[Category: Honda, Y]] | + | [[Category: Honda Y]] |
| - | [[Category: Kitaoka, M]] | + | [[Category: Kitaoka M]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Xylan degradation]]
| + | |
| Structural highlights
Function
REOX_HALH5 Hydrolyzes xylooligosaccharides with a degree of polymerization of greater than or equal to 3, releasing xylose from the reducing end. Only hydrolyzes the beta anomers of xylooligosaccharides, with inversion of anomeric configuration. Hydrolyzes the glucose and xylose-based trisaccharides where xylose is located at the -1 subsite, GXX, XXG and GXG. Does not hydrolyze xylan, chitosan, lichenan, curdlan or carboxymethylcellulose.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Glycosynthases are engineered glycoside hydrolases (GHs) that catalyse the synthesis of glycoside from glycosyl-fluoride donors and suitable acceptors. We have determined five crystal structures of the glycosynthase mutants reducing-end xylose-releasing exo-oligoxylanase, an inverting GH, that exhibit various levels of glycosynthetic activities. At the active site of the Y198F mutant, the most efficient glycosynthase, a water molecule is observed at the same position as nucleophilic water (NW) in the parent enzyme, and the loss of the fixation of the direction of the lone pair of water molecules in the mutant drastically decreases hydrolytic activity. Water molecules were also observed at each active site of the general base mutant, but they were shifted 1.0-3.0 A from the NW in the wild type. Their positions exhibited a strong correlation with the strength of glycosynthase activity. Here, we propose that a structural prerequisite for the sufficient glycosynthase reaction is the presence of a water molecule at the NW position, and mutation at the NW holder provides a general strategy for inverting GHs. The idea on the position of a water molecule may also be applicable to the design of efficient glycosynthases from retaining GHs.
Structural explanation for the acquisition of glycosynthase activity.,Hidaka M, Fushinobu S, Honda Y, Wakagi T, Shoun H, Kitaoka M J Biochem. 2010 Feb;147(2):237-44. Epub 2009 Oct 9. PMID:19819900[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Honda Y, Kitaoka M. A family 8 glycoside hydrolase from Bacillus halodurans C-125 (BH2105) is a reducing end xylose-releasing exo-oligoxylanase. J Biol Chem. 2004 Dec 31;279(53):55097-103. Epub 2004 Oct 18. PMID:15491996 doi:10.1074/jbc.M409832200
- ↑ Hidaka M, Fushinobu S, Honda Y, Wakagi T, Shoun H, Kitaoka M. Structural explanation for the acquisition of glycosynthase activity. J Biochem. 2010 Feb;147(2):237-44. Epub 2009 Oct 9. PMID:19819900 doi:10.1093/jb/mvp159
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