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| | ==Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose== | | ==Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose== |
| - | <StructureSection load='2zux' size='340' side='right' caption='[[2zux]], [[Resolution|resolution]] 1.32Å' scene=''> | + | <StructureSection load='2zux' size='340' side='right'caption='[[2zux]], [[Resolution|resolution]] 1.32Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zux]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZUX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zux]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZUX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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]] 1.32Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zuy|2zuy]]</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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yesW, BSU07050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=2zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zux OCA], [https://pdbe.org/2zux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zux RCSB], [https://www.ebi.ac.uk/pdbsum/2zux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zux 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=2zux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zux OCA], [http://pdbe.org/2zux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zux RCSB], [http://www.ebi.ac.uk/pdbsum/2zux PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/YESW_BACSU YESW_BACSU]] Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases oligosaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid, pectic acid and pectin.<ref>PMID:16682770</ref> <ref>PMID:17449691</ref> | + | [https://www.uniprot.org/uniprot/YESW_BACSU YESW_BACSU] Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases oligosaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid, pectic acid and pectin.<ref>PMID:16682770</ref> <ref>PMID:17449691</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/zu/2zux_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zu/2zux_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 globigii migula 1900]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Large Structures]] |
| - | [[Category: Itoh, T]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Mikami, B]] | + | [[Category: Itoh T]] |
| - | [[Category: Murata, K]] | + | [[Category: Mikami B]] |
| - | [[Category: Ochiai, A]] | + | [[Category: Murata K]] |
| - | [[Category: Beta-propeller]]
| + | [[Category: Ochiai A]] |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Rhamnose complex]]
| + | |
| Structural highlights
Function
YESW_BACSU Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases oligosaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid, pectic acid and pectin.[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
A saprophytic Bacillus subtilis secretes two types of rhamnogalacturonan (RG) lyases, endotype YesW and exotype YesX, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 YesW and YesX with a significant sequence identity (67.8%) cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Here we show the structural determinants for substrate recognition and the mode of action in polysaccharide lyase family 11 lyases. The crystal structures of YesW in complex with rhamnose and ligand-free YesX were determined at 1.32 and 1.65 A resolution, respectively. The YesW amino acid residues such as Asn(152), Asp(172), Asn(532), Gly(533), Thr(534), and Tyr(595) in the active cleft bind to rhamnose molecules through hydrogen bonds and van der Waals contacts. Other rhamnose molecules are accommodated at the noncatalytic domain far from the active cleft, revealing that the domain possibly functions as a novel carbohydrate-binding module. A structural comparison between YesW and YesX indicates that a specific loop in YesX for recognizing the terminal saccharide molecule sterically inhibits penetration of the polymer over the active cleft. The loop-deficient YesX mutant exhibits YesW-like endotype activity, demonstrating that molecular conversion regarding the mode of action is achieved by the addition/removal of the loop for recognizing the terminal saccharide. This is the first report on a structural insight into RG-I recognition and molecular conversion of exotype to endotype in polysaccharide lyases.
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases.,Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K J Biol Chem. 2009 Apr 10;284(15):10181-9. Epub 2009 Feb 4. PMID:19193638[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ochiai A, Yamasaki M, Itoh T, Mikami B, Hashimoto W, Murata K. Crystallization and preliminary X-ray analysis of the rhamnogalacturonan lyase YesW from Bacillus subtilis strain 168, a member of polysaccharide lyase family 11. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 May 1;62(Pt 5):438-40., Epub 2006 Apr 12. PMID:16682770 doi:http://dx.doi.org/10.1107/S1744309106011894
- ↑ Ochiai A, Itoh T, Kawamata A, Hashimoto W, Murata K. Plant cell wall degradation by saprophytic Bacillus subtilis strains: gene clusters responsible for rhamnogalacturonan depolymerization. Appl Environ Microbiol. 2007 Jun;73(12):3803-13. Epub 2007 Apr 20. PMID:17449691 doi:http://dx.doi.org/10.1128/AEM.00147-07
- ↑ Ochiai A, Itoh T, Mikami B, Hashimoto W, Murata K. Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J Biol Chem. 2009 Apr 10;284(15):10181-9. Epub 2009 Feb 4. PMID:19193638 doi:http://dx.doi.org/10.1074/jbc.M807799200
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