2okx

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(New page: 200px<br /><applet load="2okx" size="350" color="white" frame="true" align="right" spinBox="true" caption="2okx, resolution 1.90&Aring;" /> '''Crystal structure of...)
Current revision (06:29, 3 April 2024) (edit) (undo)
 
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[[Image:2okx.jpg|left|200px]]<br /><applet load="2okx" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2okx, resolution 1.90&Aring;" />
 
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'''Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A'''<br />
 
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==Overview==
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==Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A==
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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.
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<StructureSection load='2okx' size='340' side='right'caption='[[2okx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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2OKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OKX OCA].
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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]] 1.9&#8491;</td></tr>
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<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>
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==Reference==
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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=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>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17936784 17936784]
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</table>
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[[Category: Alpha-L-rhamnosidase]]
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== Function ==
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[[Category: Bacillus sp.]]
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[https://www.uniprot.org/uniprot/Q93RE7_BACGL Q93RE7_BACGL]
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Cui, Z.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Hashimoto, W.]]
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Check<jmol>
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[[Category: Mikami, B.]]
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<jmolCheckbox>
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[[Category: Murata, K.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ok/2okx_consurf.spt"</scriptWhenChecked>
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[[Category: CA]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: GOL]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: alpha barrel]]
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</jmolCheckbox>
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[[Category: glycoside hydrolase family 78]]
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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=2okx ConSurf].
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[[Category: invertase]]
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<div style="clear:both"></div>
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[[Category: rhamnosidase]]
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__TOC__
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</StructureSection>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:15:27 2008''
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[[Category: Bacillus sp. GL1]]
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[[Category: Large Structures]]
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[[Category: Cui Z]]
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[[Category: Hashimoto W]]
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[[Category: Mikami B]]
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[[Category: Murata K]]

Current revision

Crystal structure of GH78 family rhamnosidase of Bacillus SP. GL1 AT 1.9 A

PDB ID 2okx

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