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| | ==Crystal structure of xylanase XynB from Paenibacillus barcinonensis complexed with a conduramine derivative== | | ==Crystal structure of xylanase XynB from Paenibacillus barcinonensis complexed with a conduramine derivative== |
| - | <StructureSection load='3emz' size='340' side='right' caption='[[3emz]], [[Resolution|resolution]] 2.08Å' scene=''> | + | <StructureSection load='3emz' size='340' side='right'caption='[[3emz]], [[Resolution|resolution]] 2.08Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3emz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EMZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3emz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_barcinonensis Paenibacillus barcinonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EMZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HXH:(1S,2S,3R,6R)-6-[(4-PHENOXYBENZYL)AMINO]CYCLOHEX-4-ENE-1,2,3-TRIOL'>HXH</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]] 2.08Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3emc|3emc]], [[3emq|3emq]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HXH:(1S,2S,3R,6R)-6-[(4-PHENOXYBENZYL)AMINO]CYCLOHEX-4-ENE-1,2,3-TRIOL'>HXH</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xynB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=198119 Paenibacillus barcinonensis])</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=3emz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emz OCA], [https://pdbe.org/3emz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3emz RCSB], [https://www.ebi.ac.uk/pdbsum/3emz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3emz ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=3emz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3emz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3emz RCSB], [http://www.ebi.ac.uk/pdbsum/3emz PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XYNB_PAEBA XYNB_PAEBA]] Plays a role in plant xylan biodegradation, probably via the hydrolysis of short xylooligosaccharides resulting from extracellular xylan hydrolysis, once they have been transported inside cells. Shows similar activity on xylans of different rate of arabinose or methylglucuronic substitution. Also displays high activity on aryl-xylosides. Is active on xylotetraose and xylotriose, but does not hydrolyze xylobiose, indicating that XynB is a xylanase and not a beta-xylosidase.<ref>PMID:12698280</ref> <ref>PMID:8998999</ref> | + | [https://www.uniprot.org/uniprot/XYNB_PAEBA XYNB_PAEBA] Plays a role in plant xylan biodegradation, probably via the hydrolysis of short xylooligosaccharides resulting from extracellular xylan hydrolysis, once they have been transported inside cells. Shows similar activity on xylans of different rate of arabinose or methylglucuronic substitution. Also displays high activity on aryl-xylosides. Is active on xylotetraose and xylotriose, but does not hydrolyze xylobiose, indicating that XynB is a xylanase and not a beta-xylosidase.<ref>PMID:12698280</ref> <ref>PMID:8998999</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/em/3emz_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/em/3emz_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> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata 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=3emz ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3emz" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Endo-1,4-beta-xylanase]] | + | [[Category: Large Structures]] |
| | [[Category: Paenibacillus barcinonensis]] | | [[Category: Paenibacillus barcinonensis]] |
| - | [[Category: Isorna, P]] | + | [[Category: Isorna P]] |
| - | [[Category: Sanz-Aparicio, J]] | + | [[Category: Sanz-Aparicio J]] |
| - | [[Category: Gh10 enzyme complex]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
XYNB_PAEBA Plays a role in plant xylan biodegradation, probably via the hydrolysis of short xylooligosaccharides resulting from extracellular xylan hydrolysis, once they have been transported inside cells. Shows similar activity on xylans of different rate of arabinose or methylglucuronic substitution. Also displays high activity on aryl-xylosides. Is active on xylotetraose and xylotriose, but does not hydrolyze xylobiose, indicating that XynB is a xylanase and not a beta-xylosidase.[1] [2]
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
Paenibacillus barcinonensis is a soil bacterium bearing a complex set of enzymes for xylan degradation, including several secreted enzymes and Xyn10B, one of the few intracellular xylanases reported to date. The crystal structure of Xyn10B has been determined by x-ray analysis. The enzyme folds into the typical (beta/alpha)(8) barrel of family 10 glycosyl hydrolases (GH10), with additional secondary structure elements within the beta/alpha motifs. One of these loops -L7- located at the beta7 C terminus, was essential for xylanase activity as its partial deletion yielded an inactive enzyme. The loop contains residues His(249)-Glu(250), which shape a pocket opened to solvent in close proximity to the +2 subsite, which has not been described in other GH10 enzymes. This wide cavity at the +2 subsite, where methyl-2,4-pentanediol from the crystallization medium was found, is a noteworthy feature of Xyn10B, as compared with the narrow crevice described for other GH10 xylanases. Docking analysis showed that this open cavity can accommodate glucuronic acid decorations of xylo-oligosaccharides. Co-crystallization experiments with conduramine derivative inhibitors supported the importance of this open cavity at the +2 subsite for Xyn10B activity. Several mutant derivatives of Xyn10B with improved thermal stability were obtained by forced evolution. Among them, mutant xylanases S15L and M93V showed increased half-life, whereas the double mutant S15L/M93V exhibited a further increase in stability, showing a 20-fold higher heat resistance than the wild type xylanase. All the mutations obtained were located on the surface of Xyn10B. Replacement of a Ser by a Leu residue in mutant xylanase S15L can increase hydrophobic packing efficiency and fill a superficial indentation of the protein, giving rise to a more compact structure of the enzyme.
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.,Gallardo O, Pastor FI, Polaina J, Diaz P, Lysek R, Vogel P, Isorna P, Gonzalez B, Sanz-Aparicio J J Biol Chem. 2010 Jan 22;285(4):2721-33. Epub 2009 Nov 23. PMID:19940147[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gallardo O, Diaz P, Pastor FI. Characterization of a Paenibacillus cell-associated xylanase with high activity on aryl-xylosides: a new subclass of family 10 xylanases. Appl Microbiol Biotechnol. 2003 May;61(3):226-33. Epub 2003 Feb 27. PMID:12698280 doi:http://dx.doi.org/10.1007/s00253-003-1239-1
- ↑ Blanco A, Diaz P, Martinez J, Lopez O, Soler C, Pastor FI. Cloning of a Bacillus sp. BP-23 gene encoding a xylanase with high activity against aryl xylosides. FEMS Microbiol Lett. 1996 Apr 1;137(2-3):285-90. PMID:8998999
- ↑ Gallardo O, Pastor FI, Polaina J, Diaz P, Lysek R, Vogel P, Isorna P, Gonzalez B, Sanz-Aparicio J. Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution. J Biol Chem. 2010 Jan 22;285(4):2721-33. Epub 2009 Nov 23. PMID:19940147 doi:10.1074/jbc.M109.064394
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