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| | <StructureSection load='3wku' size='340' side='right'caption='[[3wku]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='3wku' size='340' side='right'caption='[[3wku]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wku]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_sp._syk-6 Sphingobium sp. syk-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WKU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wku]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_sp._SYK-6 Sphingobium sp. SYK-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WKU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</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]] 2.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vju|3vju]], [[3vjv|3vjv]], [[3vjw|3vjw]], [[3vjx|3vjx]], [[3vjy|3vjy]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GDE:3,4,5-TRIHYDROXYBENZOIC+ACID'>GDE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">desB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=627192 Sphingobium sp. SYK-6])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Linoleate_9S-lipoxygenase Linoleate 9S-lipoxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.58 1.13.11.58] </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=3wku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wku OCA], [https://pdbe.org/3wku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wku RCSB], [https://www.ebi.ac.uk/pdbsum/3wku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wku 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=3wku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wku OCA], [https://pdbe.org/3wku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wku RCSB], [https://www.ebi.ac.uk/pdbsum/3wku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wku ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/G2IKE5_SPHSK G2IKE5_SPHSK] |
| - | DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II) ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5) of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.
| + | |
| - | | + | |
| - | Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6.,Sugimoto K, Senda M, Kasai D, Fukuda M, Masai E, Senda T PLoS One. 2014 Mar 21;9(3):e92249. doi: 10.1371/journal.pone.0092249. eCollection, 2014. PMID:24657997<ref>PMID:24657997</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3wku" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Linoleate 9S-lipoxygenase]]
| + | [[Category: Sphingobium sp. SYK-6]] |
| - | [[Category: Sphingobium sp. syk-6]] | + | [[Category: Fukuda M]] |
| - | [[Category: Fukuda, M]] | + | [[Category: Kasai D]] |
| - | [[Category: Kasai, D]] | + | [[Category: Masai E]] |
| - | [[Category: Masai, E]] | + | [[Category: Senda M]] |
| - | [[Category: Senda, M]] | + | [[Category: Senda T]] |
| - | [[Category: Senda, T]] | + | [[Category: Sugimoto K]] |
| - | [[Category: Sugimoto, K]] | + | |
| - | [[Category: Domain-swap dimer]]
| + | |
| - | [[Category: Extradiol dioxygenase]]
| + | |
| - | [[Category: Fe2+ binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Type ii extradiol dioxygenase]]
| + | |
