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| - | [[Image:2okx.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A== |
| - | |PDB= 2okx |SIZE=350|CAPTION= <scene name='initialview01'>2okx</scene>, resolution 1.90Å
| + | <StructureSection load='2okx' size='340' side='right'caption='[[2okx]], [[Resolution|resolution]] 1.90Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
| + | <table><tr><td colspan='2'>[[2okx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._GL1 Bacillus sp. GL1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OKX FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-L-rhamnosidase Alpha-L-rhamnosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.40 3.2.1.40] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | |GENE= rhaB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])
| + | <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=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2okx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2okx OCA], [https://pdbe.org/2okx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2okx RCSB], [https://www.ebi.ac.uk/pdbsum/2okx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2okx ProSAT]</span></td></tr> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2okx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2okx OCA], [http://www.ebi.ac.uk/pdbsum/2okx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2okx RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q93RE7_BACGL Q93RE7_BACGL] |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/2okx_consurf.spt"</scriptWhenChecked> |
| - | alpha-L-Rhamnosidase (EC 3.2.1.40) catalyzes the hydrolytic release of rhamnose from polysaccharides and glycosides. Bacillus sp. GL1 alpha-L-rhamnosidase (RhaB), a member of glycoside hydrolase (GH) family 78, is responsible for degrading the bacterial biofilm gellan, and also functions as a debittering agent for citrus fruit in the food and beverage industries through the release of rhamnose from plant glycoside, naringin. The X-ray crystal structure of RhaB was determined by single-wavelength anomalous diffraction using a selenomethionine derivative and refined at 1.9 A resolution with a final R-factor of 18.2%. As is seen in the homodimeric form of the active enzyme, the structure of RhaB in crystal packing is a homodimer containing 1908 amino acids (residues 3-956), 43 glycerol molecules, four calcium ions, and 1755 water molecules. The overall structure consists of five domains, four of which are beta-sandwich structures designated as domains N, D1, D2, and C, and an (alpha/alpha)(6)-barrel structure designated as domain A. Structural comparison by DALI showed that RhaB shares its highest level of structural similarity with chitobiose phosphorylase (Z score of 25.3). The structure of RhaB in complex with the reaction product rhamnose (inhibitor constant, K(i)=1.8 mM) was also determined and refined at 2.1 A with a final R-factor of 19.5%. Rhamnose is bound to the deep cleft of the (alpha/alpha)(6)-barrel domain, as is seen in the clan-L GHs. Several negatively charged residues, such as Asp567, Glu572, Asp579, and Glu841, conserved in GH family 78 enzymes, interact with rhamnose, and RhaB mutants of these residues have drastically reduced enzyme activity, indicating that the residues are crucial for enzyme catalysis and/or substrate binding. To our knowledge, this is the first report on the determination of the crystal structure of alpha-L-rhamnosidase and identification of its clan-L (alpha/alpha)(6)-barrel as a catalytic domain.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 2OKX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKX OCA].
| + | </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=2okx ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference==
| + | __TOC__ |
| - | Crystal structure of glycoside hydrolase family 78 alpha-L-Rhamnosidase from Bacillus sp. GL1., Cui Z, Maruyama Y, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2007 Nov 23;374(2):384-98. Epub 2007 Sep 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17936784 17936784]
| + | </StructureSection> |
| - | [[Category: Alpha-L-rhamnosidase]]
| + | [[Category: Bacillus sp. GL1]] |
| - | [[Category: Bacillus sp.]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]] | + | [[Category: Cui Z]] |
| - | [[Category: Cui, Z.]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Hashimoto, W.]] | + | [[Category: Mikami B]] |
| - | [[Category: Mikami, B.]] | + | [[Category: Murata K]] |
| - | [[Category: Murata, K.]] | + | |
| - | [[Category: alpha barrel]]
| + | |
| - | [[Category: glycoside hydrolase family 78]]
| + | |
| - | [[Category: invertase]]
| + | |
| - | [[Category: rhamnosidase]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:19:21 2008''
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