2bfg

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[[Image:2bfg.gif|left|200px]]
 
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{{Structure
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==crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside==
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|PDB= 2bfg |SIZE=350|CAPTION= <scene name='initialview01'>2bfg</scene>, resolution 2.40&Aring;
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<StructureSection load='2bfg' size='340' side='right'caption='[[2bfg]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Chain+H'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=ANX:2,5-DINITROPHENOL'>ANX</scene>
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<table><tr><td colspan='2'>[[2bfg]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BFG FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37]
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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]] 2.4&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANX:2,5-DINITROPHENOL'>ANX</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=2bfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bfg OCA], [https://pdbe.org/2bfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bfg RCSB], [https://www.ebi.ac.uk/pdbsum/2bfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bfg ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/XYNB_GEOSE XYNB_GEOSE]
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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/bf/2bfg_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=2bfg 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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Beta-D-Xylosidases are glycoside hydrolases that catalyse the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicelluloses. beta-D-Xylosidases are found in glycoside hydrolase families 3, 39, 43, 52 and 54. The first crystal structure of a GH39 beta-xylosidase revealed a multi-domain organization with the catalytic domain having the canonical (beta/alpha)8 barrel fold. Here, we report the crystal structure of the GH39 Geobacillus stearothermophilus beta-D-xylosidase, inactivated by a point mutation of the general acid-base residue E160A, in complex with the chromogenic substrate molecule 2,5-dinitrophenyl-beta-D-xyloside. Surprisingly, six of the eight active sites present in the crystallographic asymmetric unit contain the trapped covalent glycosyl-enzyme intermediate, while two of them still contain the uncleaved substrate. The structural characterization of these two critical species along the reaction coordinate of this enzyme identifies the residues forming its xyloside-binding pocket as well as those essential for its aglycone recognition.
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'''CRYSTAL STRUCTURE OF BETA-XYLOSIDASE (FAM GH39) IN COMPLEX WITH DINITROPHENYL-BETA-XYLOSIDE AND COVALENTLY BOUND XYLOSIDE'''
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Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus.,Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y J Mol Biol. 2005 Nov 4;353(4):838-46. Epub 2005 Sep 20. PMID:16212978<ref>PMID:16212978</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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</div>
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<div class="pdbe-citations 2bfg" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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Beta-D-Xylosidases are glycoside hydrolases that catalyse the release of xylose units from short xylooligosaccharides and are engaged in the final breakdown of plant cell-wall hemicelluloses. beta-D-Xylosidases are found in glycoside hydrolase families 3, 39, 43, 52 and 54. The first crystal structure of a GH39 beta-xylosidase revealed a multi-domain organization with the catalytic domain having the canonical (beta/alpha)8 barrel fold. Here, we report the crystal structure of the GH39 Geobacillus stearothermophilus beta-D-xylosidase, inactivated by a point mutation of the general acid-base residue E160A, in complex with the chromogenic substrate molecule 2,5-dinitrophenyl-beta-D-xyloside. Surprisingly, six of the eight active sites present in the crystallographic asymmetric unit contain the trapped covalent glycosyl-enzyme intermediate, while two of them still contain the uncleaved substrate. The structural characterization of these two critical species along the reaction coordinate of this enzyme identifies the residues forming its xyloside-binding pocket as well as those essential for its aglycone recognition.
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*[[Xylosidase 3D structures|Xylosidase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2BFG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BFG OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Enzyme-substrate complex structures of a GH39 beta-xylosidase from Geobacillus stearothermophilus., Czjzek M, Ben David A, Bravman T, Shoham G, Henrissat B, Shoham Y, J Mol Biol. 2005 Nov 4;353(4):838-46. Epub 2005 Sep 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16212978 16212978]
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[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Xylan 1,4-beta-xylosidase]]
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[[Category: Bravman T]]
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[[Category: Bravman, T.]]
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[[Category: Czjzek M]]
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[[Category: Czjzek, M.]]
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[[Category: Henrissat B]]
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[[Category: Henrissat, B.]]
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[[Category: Shoham Y]]
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[[Category: Shoham, Y.]]
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[[Category: ANX]]
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[[Category: NA]]
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[[Category: SO4]]
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[[Category: XYS]]
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[[Category: beta-xylosidase]]
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[[Category: complex of the covalent intermediate]]
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[[Category: enzyme/substrate complex]]
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[[Category: family gh39]]
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[[Category: hydrolase]]
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[[Category: thermophilic enzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:01:16 2008''
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Current revision

crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside

PDB ID 2bfg

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