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| <StructureSection load='2eab' size='340' side='right'caption='[[2eab]], [[Resolution|resolution]] 1.12Å' scene=''> | | <StructureSection load='2eab' size='340' side='right'caption='[[2eab]], [[Resolution|resolution]] 1.12Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[2eab]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinobacterium_bifidum"_(tissier_1900)_puntoni_1937 "actinobacterium bifidum" (tissier 1900) puntoni 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EAB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2eab]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum Bifidobacterium bifidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EAB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EAB 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.12Å</td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2eac|2eac]], [[2ead|2ead]], [[2eae|2eae]], [[2eaf|2eaf]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
- | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,2-alpha-L-fucosidase 1,2-alpha-L-fucosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.63 3.2.1.63] </span></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=2eab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eab OCA], [https://pdbe.org/2eab PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eab RCSB], [https://www.ebi.ac.uk/pdbsum/2eab PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eab 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=2eab FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eab OCA], [http://pdbe.org/2eab PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eab RCSB], [http://www.ebi.ac.uk/pdbsum/2eab PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2eab ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| + | == Function == |
| + | [https://www.uniprot.org/uniprot/Q6JV24_BIFBI Q6JV24_BIFBI] |
| == Evolutionary Conservation == | | == Evolutionary Conservation == |
| [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| <jmolCheckbox> | | <jmolCheckbox> |
| <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2eab_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ea/2eab_consurf.spt"</scriptWhenChecked> |
- | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| </jmolCheckbox> | | </jmolCheckbox> |
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
- | [[Category: 1,2-alpha-L-fucosidase]] | + | [[Category: Bifidobacterium bifidum]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Katayama, T]] | + | [[Category: Katayama T]] |
- | [[Category: Kato, R]] | + | [[Category: Kato R]] |
- | [[Category: Nagae, M]] | + | [[Category: Nagae M]] |
- | [[Category: Tsuchiya, A]] | + | [[Category: Tsuchiya A]] |
- | [[Category: Wakatsuki, S]] | + | [[Category: Wakatsuki S]] |
- | [[Category: Yamamoto, K]] | + | [[Category: Yamamoto K]] |
- | [[Category: Fucosidase]]
| + | |
- | [[Category: Glycoside hydrolase]]
| + | |
- | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
Q6JV24_BIFBI
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
1,2-alpha-L-fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95. To better understand the molecular mechanism of this enzyme, we determined the x-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 probably acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.
Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum.,Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:17459873[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, Kato R. Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. J Biol Chem. 2007 Jun 22;282(25):18497-509. Epub 2007 Apr 25. PMID:17459873 doi:10.1074/jbc.M702246200
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