1h4h

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[[Image:1h4h.gif|left|200px]]
 
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{{Structure
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==Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre==
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|PDB= 1h4h |SIZE=350|CAPTION= <scene name='initialview01'>1h4h</scene>, resolution 1.90&Aring;
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<StructureSection load='1h4h' size='340' side='right'caption='[[1h4h]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE= <scene name='pdbsite=BC3:Xys+Binding+Site+For+Residue+D1211'>BC3</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene>
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<table><tr><td colspan='2'>[[1h4h]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salipaludibacillus_agaradhaerens Salipaludibacillus agaradhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H4H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H4H FirstGlance]. <br>
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|ACTIVITY= <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>
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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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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
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|DOMAIN=
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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=1h4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h4h OCA], [https://pdbe.org/1h4h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h4h RCSB], [https://www.ebi.ac.uk/pdbsum/1h4h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h4h ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h4h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h4h OCA], [http://www.ebi.ac.uk/pdbsum/1h4h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1h4h RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/Q7SIE2_SALAG Q7SIE2_SALAG]
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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/h4/1h4h_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1h4h 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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BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates. RESULTS: The structure of the family 11 xylanase, Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A resolution, respectively. The covalent glycosyl-enzyme intermediate has been trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike covalent intermediate structures for glycoside hydrolases from other families, the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation observed for other systems, is consistent with the stereochemical constraints required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11 covalent glycosyl-enzyme intermediate with the equivalent structure for the related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the likely determinants for substrate specificity in this clan of glycoside hydrolases.
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'''OLIGOSACCHARIDE-BINDING TO FAMILY 11 XYLANASES: BOTH COVALENT INTERMEDIATE AND MUTANT-PRODUCT COMPLEXES DISPLAY 2,5B CONFORMATIONS AT THE ACTIVE-CENTRE'''
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Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.,Sabini E, Sulzenbacher G, Dauter M, Dauter Z, Jorgensen PL, Schulein M, Dupont C, Davies GJ, Wilson KS Chem Biol. 1999 Jul;6(7):483-92. PMID:10381409<ref>PMID:10381409</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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==Overview==
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</div>
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The glycoside hydrolase sequence-based classification reveals two families of enzymes which hydrolyse the beta-1,4-linked backbone of xylan, xylanases, termed families GH-10 and GH-11. Family GH-11 xylanases are intriguing in that catalysis is performed via a covalent intermediate adopting an unusual (2,5)B (boat) conformation, a conformation which also fulfils the stereochemical constraints of the oxocarbenium ion-like transition state. Here, the 1.9 A structure of a nucleophile, E94A, mutant of the Xyn11 from Bacillus agaradhaerens in complex with xylotriose is presented. Intriguingly, this complex also adopts the (2,5)B conformation in the -1 subsite, with the vacant space provided by the Glu--&gt;Ala mutation allowing the sugar to adopt the alpha-configuration at C1. The structure of the covalent 2-deoxy-2-fluoroxylobiosyl-enzyme intermediate has been extended to atomic (1.1 A) resolution.
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<div class="pdbe-citations 1h4h" style="background-color:#fffaf0;"></div>
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== References ==
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==About this Structure==
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<references/>
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1H4H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_agaradhaerens Bacillus agaradhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H4H OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre., Sabini E, Wilson KS, Danielsen S, Schulein M, Davies GJ, Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1344-7. Epub 2001, Aug 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11526340 11526340]
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[[Category: Salipaludibacillus agaradhaerens]]
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[[Category: Bacillus agaradhaerens]]
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[[Category: Danielsen S]]
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[[Category: Endo-1,4-beta-xylanase]]
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[[Category: Davies GJ]]
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[[Category: Single protein]]
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[[Category: Sabini E]]
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[[Category: Danielsen, S.]]
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[[Category: Schulein M]]
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[[Category: Davies, G J.]]
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[[Category: Wilson KS]]
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[[Category: Sabini, E.]]
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[[Category: Schulein, M.]]
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[[Category: Wilson, K S.]]
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[[Category: boat conformation]]
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[[Category: intermediate]]
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[[Category: mutant]]
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[[Category: oligosaccharide]]
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[[Category: transition-state]]
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[[Category: xylanase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:57:30 2008''
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Current revision

Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre

PDB ID 1h4h

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