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| | <StructureSection load='3nvc' size='340' side='right'caption='[[3nvc]], [[Resolution|resolution]] 2.45Å' scene=''> | | <StructureSection load='3nvc' size='340' side='right'caption='[[3nvc]], [[Resolution|resolution]] 2.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3nvc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cip_106963 Cip 106963]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3nvc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudaminobacter_salicylatoxidans Pseudaminobacter salicylatoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</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]] 2.45Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2phd|2phd]], [[3njz|3njz]], [[3nkt|3nkt]], [[3nl1|3nl1]], [[3nst|3nst]], [[3nw4|3nw4]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Gentisate_1,2-dioxygenase Gentisate 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.4 1.13.11.4] </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=3nvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvc OCA], [https://pdbe.org/3nvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvc RCSB], [https://www.ebi.ac.uk/pdbsum/3nvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvc 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=3nvc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvc OCA], [https://pdbe.org/3nvc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvc RCSB], [https://www.ebi.ac.uk/pdbsum/3nvc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q67FT0_PSESE Q67FT0_PSESE] |
| | <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: Cip 106963]] | |
| - | [[Category: Gentisate 1,2-dioxygenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Briganti, F]] | + | [[Category: Pseudaminobacter salicylatoxidans]] |
| - | [[Category: Ferraroni, M]] | + | [[Category: Briganti F]] |
| - | [[Category: Matera, I]] | + | [[Category: Ferraroni M]] |
| - | [[Category: Beta-barrel]] | + | [[Category: Matera I]] |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
Q67FT0_PSESE
Publication Abstract from PubMed
UNLABELLED: The salicylate 1,2-dioxygenase (SDO) from the bacterium Pseudaminobacter salicylatoxidans BN12 is a versatile gentisate 1,2-dioxygenase (GDO) that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates. Several variants of this enzyme were rationally designed based on the previously determined enzyme structure and sequence differences between the SDO and the 'conventional' GDO from Corynebacterium glutamicum. This was undertaken in order to define the structural elements that give the SDO its unique ability to dioxygenolytically cleave (substituted) salicylates. SDO variants M103L, G106A, G111A, R113G, S147R and F159Y were constructed and it was found that G106A oxidized only gentisate; 1-hydroxy-2-naphthoate and salicylate were not converted. This indicated that this enzyme variant behaves like previously known 'conventional' GDOs. Crystals of the G106A SDO variant and its complexes with salicylate and gentisate were obtained under anaerobic conditions, and the structures were solved and analyzed. The amino acid residue Gly106 is located inside the SDO active site cavity but does not directly interact with the substrates. Crystal structures of G106A SDO complexes with gentisate and salicylate showed a different binding mode for salicylate when compared with the wild-type enzyme. Thus, salicylate coordinated in the G106A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that was formed between Trp104 and Asp174 in the G106A variant. It is proposed that this type of unproductive substrate binding might generally limit the substrate spectrum of 'conventional' GDOs. DATABASE: Structural data are available in the Protein Data Bank databases under the accession numbers 3NST, 3NWA, 3NVC.
The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate.,Ferraroni M, Matera I, Burger S, Reichert S, Steimer L, Scozzafava A, Stolz A, Briganti F FEBS J. 2013 Apr;280(7):1643-52. doi: 10.1111/febs.12173. Epub 2013 Feb 28. PMID:23384287[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ferraroni M, Matera I, Burger S, Reichert S, Steimer L, Scozzafava A, Stolz A, Briganti F. The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate. FEBS J. 2013 Apr;280(7):1643-52. doi: 10.1111/febs.12173. Epub 2013 Feb 28. PMID:23384287 doi:http://dx.doi.org/10.1111/febs.12173
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