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| | <StructureSection load='7dfs' size='340' side='right'caption='[[7dfs]], [[Resolution|resolution]] 1.49Å' scene=''> | | <StructureSection load='7dfs' size='340' side='right'caption='[[7dfs]], [[Resolution|resolution]] 1.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7dfs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_144134 Cbs 144134]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFS FirstGlance]. <br> | + | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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]] 1.49Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FobglcA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5507 CBS 144134])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=GCU:D-GLUCURONIC+ACID'>GCU</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-glucuronidase Beta-glucuronidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.31 3.2.1.31] </span></td></tr>
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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=7dfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfs OCA], [https://pdbe.org/7dfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dfs RCSB], [https://www.ebi.ac.uk/pdbsum/7dfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfs ProSAT]</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=7dfs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dfs OCA], [https://pdbe.org/7dfs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dfs RCSB], [https://www.ebi.ac.uk/pdbsum/7dfs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dfs ProSAT]</span></td></tr> |
| | </table> | | </table> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Beta-glucuronidase]] | |
| - | [[Category: Cbs 144134]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arakawa, T]] | + | [[Category: Arakawa T]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Kondo, T]] | + | [[Category: Kondo T]] |
| - | [[Category: Sakamoto, T]] | + | [[Category: Sakamoto T]] |
| - | [[Category: Antiparallel beta-sheet]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.49Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
In this study, we have isolated the novel enzyme 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase (FoBGlcA), which releases alpha-l-rhamnosyl (1-->4) glucuronic acid from gum arabic (GA), from Fusarium oxysporum 12S culture supernatant, and for the first time report an enzyme with such catalytic activity. The gene encoding FoBGlcA was cloned and expressed in Pichia pastoris. When GA was subjected to the recombinant enzyme, > 95% of the l-rhamnose (Rha) and d-glucuronic acid in the substrate were released, which indicates that almost all Rha binds to the glucuronic acid at the end of the GA side chains. The crystal structure of FoBGlcA was determined using a single-wavelength anomalous dispersion at 1.51 A resolution. FoBGlcA consisted of an N-terminal (beta/alpha)8 -barrel domain and a C-terminal antiparallel beta-sheet domain. This configuration is characteristic of glycoside hydrolase (GH) family 79 proteins. A structural similarity search showed that FoBGlcA mostly resembled GH79 beta-d-glucuronidase (AcGlcA79A) of Acidobacterium capsulatum; however, the root-mean-square deviation value was 3.2 A, indicating that FoBGlcA has a high structural divergence. FoBGlcA had a low sequence identity with AcGlcA79A (19%) and differed from other GH79 beta-glucuronidases. The structures of FoBGlcA and AcGlcA79A also differed in terms of the loop structure location near subsite -2 of their catalytic sites, which may account for the unique substrate specificity of FoBGlcA. The amino acid residues involved in the catalytic activity of this enzyme were determined by evaluating the activity levels of various mutant enzymes based on the crystal structure analysis of the FoBGlcA reaction product complex. DATABASE: Atomic coordinates and structure factors (codes 7DFQ and 7DFS) have been deposited in the Protein Data Bank (http://wwpdb.org/).
Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum.,Kondo T, Kichijo M, Nakaya M, Takenaka S, Arakawa T, Kotake T, Fushinobu S, Sakamoto T FEBS J. 2021 Mar 1. doi: 10.1111/febs.15795. PMID:33645879[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kondo T, Kichijo M, Nakaya M, Takenaka S, Arakawa T, Kotake T, Fushinobu S, Sakamoto T. Biochemical and structural characterization of a novel 4-O-alpha-l-rhamnosyl-beta-d-glucuronidase from Fusarium oxysporum. FEBS J. 2021 Mar 1. doi: 10.1111/febs.15795. PMID:33645879 doi:http://dx.doi.org/10.1111/febs.15795
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