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| | ==Complex structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum with arabinobiose== | | ==Complex structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum with arabinobiose== |
| - | <StructureSection load='2w5o' size='340' side='right' caption='[[2w5o]], [[Resolution|resolution]] 2.05Å' scene=''> | + | <StructureSection load='2w5o' size='340' side='right'caption='[[2w5o]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2w5o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusairum_graminearum Fusairum graminearum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W5O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2w5o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_graminearum Fusarium graminearum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W5O FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.05Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2w5n|2w5n]]</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=2w5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w5o OCA], [https://pdbe.org/2w5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w5o RCSB], [https://www.ebi.ac.uk/pdbsum/2w5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w5o ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-reducing_end_alpha-L-arabinofuranosidase Non-reducing end alpha-L-arabinofuranosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.55 3.2.1.55] </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=2w5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w5o OCA], [http://pdbe.org/2w5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w5o RCSB], [http://www.ebi.ac.uk/pdbsum/2w5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w5o ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | ==See Also== | | ==See Also== |
| - | *[[Arabinanase|Arabinanase]] | + | *[[Arabinanase 3D structures|Arabinanase 3D structures]] |
| - | *[[Exo-alpha-1%2C5-L-Arabinanase|Exo-alpha-1%2C5-L-Arabinanase]]
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Fusairum graminearum]] | + | [[Category: Fusarium graminearum]] |
| - | [[Category: Non-reducing end alpha-L-arabinofuranosidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Byrns, S C]] | + | [[Category: Byrns SC]] |
| - | [[Category: Carapito, R]] | + | [[Category: Carapito R]] |
| - | [[Category: Imberty, A]] | + | [[Category: Imberty A]] |
| - | [[Category: Jeltsch, J M]] | + | [[Category: Jeltsch JM]] |
| - | [[Category: Lowary, T L]] | + | [[Category: Lowary TL]] |
| - | [[Category: Phalip, V]] | + | [[Category: Phalip V]] |
| - | [[Category: Tam, P H]] | + | [[Category: Tam PH]] |
| - | [[Category: Varrot, A]] | + | [[Category: Varrot A]] |
| - | [[Category: Alpha-l-arabinofuranosidase]]
| + | |
| - | [[Category: Arabinobiose]]
| + | |
| - | [[Category: Gh93]]
| + | |
| - | [[Category: Glycosyl hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
2w5o is a 1 chain structure with sequence from Fusarium graminearum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.05Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
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
The phytopathogenic fungus Fusarium graminearum secretes a very diverse pool of glycoside hydrolases (GHs) aimed at degrading plant cell walls. alpha-l-Arabinanases are essential GHs participating in the complete hydrolysis of hemicellulose, a natural resource for various industrial processes, such as bioethanol or pharmaceuticals production. Arb93A, the exo-1,5-alpha-l-arabinanase of F. graminearum encoded by the gene fg03054.1, belongs to the GH93 family, for which no structural data exists. The enzyme is highly active (1065 units/mg) and displays a strict substrate specificity for linear alpha-1,5-l-arabinan. Biochemical assays and NMR experiments demonstrated that the enzyme releases alpha-1,5-l-arabinobiose from the nonreducing end of the polysaccharide. We determined the crystal structure of the native enzyme and its complex with alpha-1,5-l-arabinobiose, a degradation product of alpha-Me-1,5-l-arabinotetraose, at 1.85 and 2.05A resolution, respectively. Arb93A is a monomeric enzyme, which presents the six-bladed beta-propeller fold characteristic of sialidases of clan GHE. The configuration of the bound arabinobiose is consistent with the retaining mechanism proposed for the GH93 family. Catalytic residues were proposed from the structural analysis, and site-directed mutagenesis was used to validate their role. They are significantly different from those observed for GHE sialidases.
Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase.,Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, Phalip V J Biol Chem. 2009 May 1;284(18):12285-96. Epub 2009 Mar 6. PMID:19269961[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Carapito R, Imberty A, Jeltsch JM, Byrns SC, Tam PH, Lowary TL, Varrot A, Phalip V. Molecular basis of arabinobio-hydrolase activity in phytopathogenic fungi: crystal structure and catalytic mechanism of Fusarium graminearum GH93 exo-alpha-L-arabinanase. J Biol Chem. 2009 May 1;284(18):12285-96. Epub 2009 Mar 6. PMID:19269961 doi:10.1074/jbc.M900439200
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