2drs

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[[Image:2drs.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S mutant==
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|PDB= 2drs |SIZE=350|CAPTION= <scene name='initialview01'>2drs</scene>, resolution 2.10&Aring;
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<StructureSection load='2drs' size='340' side='right'caption='[[2drs]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[2drs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans_C-125 Alkalihalobacillus halodurans C-125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DRS FirstGlance]. <br>
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|ACTIVITY= [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]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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|GENE= BH2105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86665 Bacillus halodurans])
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<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>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2drs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2drs OCA], [https://pdbe.org/2drs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2drs RCSB], [https://www.ebi.ac.uk/pdbsum/2drs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2drs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/2drs_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2drs ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S mutant'''
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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<ref>PMID:19819900</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==Overview==
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</div>
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Reducing end xylose-releasing exooligoxylanase (Rex, EC 3.2.1.156) is an inverting GH that hydrolyzes xylooligosaccharides (&gt; or = X3) to release X1 at their reducing end. The wild-type enzyme exhibited the Hehre resynthesis hydrolysis mechanism, in which alpha-X2F was hydrolyzed to X2 and HF in the presence of X1 as an acceptor molecule. However, the transglycosidation product (X3) was not detectable in the reaction. To convert reducing end xylose-releasing exooligoxylanase to glycosynthase, derivatives with mutations in the catalytic base (Asp-263) were constructed by saturation random mutagenesis. Nine amino acid residue mutants (Asp-263 to Gly, Ala, Val, Thr, Leu, Asn, Cys, Pro, or Ser) were found to possess glycosynthase activity forming X3 from alpha-X2F and X1. Among them, D263C showed the highest level of X3 production, and D263N exhibited the fastest consumption of alpha-X2F. The D263C mutant showed 10-fold lower hydrolytic activity than D263N, resulting in the highest yield of X3. X2 was formed from the early stage of the reaction of the D263C mutant, indicating that a portion of the X3 formed by condensation was hydrolyzed before its release from the enzyme. To acquire glycosynthase activity from inverting enzymes, it is important to minimize the decrease in F(-)-releasing activity while maximizing the decrease in the hydrolytic activity. The present study expands the possibility of conversion of glycosynthases from inverting enzymes.
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<div class="pdbe-citations 2drs" style="background-color:#fffaf0;"></div>
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== References ==
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==About this Structure==
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<references/>
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2DRS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRS OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Alkalihalobacillus halodurans C-125]]
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The first glycosynthase derived from an inverting glycoside hydrolase., Honda Y, Kitaoka M, J Biol Chem. 2006 Jan 20;281(3):1426-31. Epub 2005 Nov 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16301312 16301312]
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[[Category: Large Structures]]
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[[Category: Bacillus halodurans]]
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[[Category: Fushinobu S]]
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[[Category: Oligosaccharide reducing-end xylanase]]
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[[Category: Hidaka M]]
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[[Category: Single protein]]
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[[Category: Honda Y]]
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[[Category: Fushinobu, S.]]
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[[Category: Kitaoka M]]
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[[Category: Hidaka, M.]]
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[[Category: Shoun H]]
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[[Category: Honda, Y.]]
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[[Category: Wakagi T]]
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[[Category: Kitaoka, M.]]
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[[Category: Shoun, H.]]
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[[Category: Wakagi, T.]]
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[[Category: GOL]]
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[[Category: NI]]
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[[Category: (alpla/alpha)6 barrel]]
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[[Category: glycoside hydrolase family 8]]
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[[Category: national project on protein structural and functional analyse]]
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[[Category: nppsfa]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:30:50 2008''
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Current revision

Crystal structure of reducing-end-xylose releasing exo-oligoxylanase D263S mutant

PDB ID 2drs

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