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| | ==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with Raffinose== | | ==Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with Raffinose== |
| - | <StructureSection load='5fkc' size='340' side='right' caption='[[5fkc]], [[Resolution|resolution]] 1.82Å' scene=''> | + | <StructureSection load='5fkc' size='340' side='right'caption='[[5fkc]], [[Resolution|resolution]] 1.82Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5fkc]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FKC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FKC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5fkc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phaffia_rhodozyma Phaffia rhodozyma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FKC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 1.82Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ann|5ann]], [[5fix|5fix]], [[5fk7|5fk7]], [[5fk8|5fk8]], [[5fkb|5fkb]], [[5fmb|5fmb]], [[5fmc|5fmc]], [[5fmd|5fmd]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900002:raffinose'>PRD_900002</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-fructofuranosidase Beta-fructofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.26 3.2.1.26] </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=5fkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkc OCA], [https://pdbe.org/5fkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fkc RCSB], [https://www.ebi.ac.uk/pdbsum/5fkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fkc 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=5fkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fkc OCA], [http://pdbe.org/5fkc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fkc RCSB], [http://www.ebi.ac.uk/pdbsum/5fkc PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/J7HDY4_PHARH J7HDY4_PHARH] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-fructofuranosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Ramirez-Escudero, M]] | + | [[Category: Phaffia rhodozyma]] |
| - | [[Category: Sanz-Aparicio, J]] | + | [[Category: Ramirez-Escudero M]] |
| - | [[Category: Amino acid sequence]]
| + | [[Category: Sanz-Aparicio J]] |
| - | [[Category: Carbohydrate]]
| + | |
| - | [[Category: Catalysis]]
| + | |
| - | [[Category: Catalytic domain]]
| + | |
| - | [[Category: Cloning]]
| + | |
| - | [[Category: Dimerization]]
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| - | [[Category: Fungal protein]]
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| - | [[Category: Glycoside hydrolase]]
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| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Invertase]]
| + | |
| - | [[Category: Kinetic]]
| + | |
| - | [[Category: Molecular]]
| + | |
| - | [[Category: Molecular conformation]]
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| - | [[Category: Pichia pastori]]
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| - | [[Category: Prebiotic]]
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| - | [[Category: Protein conformation]]
| + | |
| - | [[Category: Protein structure]]
| + | |
| - | [[Category: Quaternary]]
| + | |
| - | [[Category: Raffinose]]
| + | |
| - | [[Category: Secondary]]
| + | |
| - | [[Category: Substrate specificity]]
| + | |
| Structural highlights
5fkc is a 2 chain structure with sequence from Phaffia rhodozyma. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.82Å |
| Ligands: | , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
J7HDY4_PHARH
Publication Abstract from PubMed
Xanthophyllomyces dendrorhous beta-fructofuranosidase (XdINV) is a highly glycosylated dimeric enzyme that hydrolyzes sucrose and releases fructose from various fructooligosaccharides (FOS) and fructans. It also catalyzes the synthesis of FOS, prebiotics that stimulate the growth of beneficial bacteria in human gut. In contrast to most fructosylating enzymes, XdINV produces neo-FOS, which makes it an interesting biotechnology target. We present here its three-dimensional structure, which shows the expected bimodular arrangement but, also, a long extension of its C-terminus that together with a N-linked glycan mediate the formation of an unusual dimer. This dimer shapes two active sites communicated by a long channel, which might indicate its potential ability to house branched fructans. This arrangement could be representative of a group of GH32 yeast enzymes having the traits observed in XdINV. Inactivated D80A mutant was used to obtain complexes with relevant substrates and products, their crystals structures showing at least four binding subsites at each active site. Moreover, two different positions are observed from subsite +2 depending of the substrate and, thus, a flexible loop (Glu334-His343) is essential in binding sucrose and beta(2-1) linked oligosaccharides. Conversely, beta(2-6) and neo-type substrates are accommodated mainly by stacking to Trp105, explaining the production of neokestose and the efficient fructosylating activity of XdINV on alpha-glucosides. The role of relevant residues has been investigated by mutagenesis and kinetics measurements and a model for the transfructosylating reaction has been proposed. The plasticity of its active site makes XdINV a valuable and flexible biocatalyst to produce novel bioconjugates.
Structural analysis of beta-fructofuranosidase from Xanthophyllomyces dendrorhous reveals unique features and the crucial role of N-glycosylation in oligomerization and activity.,Ramirez-Escudero M, Gimeno-Perez M, Gonzalez B, Linde D, Merdzo Z, Fernandez-Lobato M, Sanz-Aparicio J J Biol Chem. 2016 Jan 28. pii: jbc.M115.708495. PMID:26823463[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Ramirez-Escudero M, Gimeno-Perez M, Gonzalez B, Linde D, Merdzo Z, Fernandez-Lobato M, Sanz-Aparicio J. Structural analysis of beta-fructofuranosidase from Xanthophyllomyces dendrorhous reveals unique features and the crucial role of N-glycosylation in oligomerization and activity. J Biol Chem. 2016 Jan 28. pii: jbc.M115.708495. PMID:26823463 doi:http://dx.doi.org/10.1074/jbc.M115.708495
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