3nw4

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Revision as of 08:08, 4 November 2020

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with gentisate

Structural highlights

3nw4 is a 1 chain structure with sequence from Cip 106963. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2phd, 3njz, 3nkt, 3nl1, 3nst, 3nvc
Activity:	Gentisate 1,2-dioxygenase, with EC number 1.13.11.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3nw4"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with gentisate==
-<StructureSection load='3nw4' size='340' side='right' caption='[[3nw4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3nw4' size='340' side='right'caption='[[3nw4]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nw4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106963 Cip 106963]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NW4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NW4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nw4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_106963 Cip 106963]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NW4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3NW4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTQ:2,5-DIHYDROXYBENZOIC+ACID'>GTQ</scene></td></tr>
+</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=GTQ:2,5-DIHYDROXYBENZOIC+ACID'>GTQ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2phd|2phd]], [[3njz|3njz]], [[3nkt|3nkt]], [[3nl1|3nl1]], [[3nst|3nst]], [[3nvc|3nvc]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gentisate_1,2-dioxygenase Gentisate 1,2-dioxygenase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nw4 OCA], [http://pdbe.org/3nw4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nw4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nw4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nw4 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3nw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nw4 OCA], [http://pdbe.org/3nw4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nw4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nw4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nw4 ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Dioxygenase|Dioxygenase]]
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
 == References ==
 <references/>
@@ Line 27: / Line 27: @@
 [[Category: Cip 106963]]
 [[Category: Gentisate 1,2-dioxygenase]]
+[[Category: Large Structures]]
 [[Category: Briganti, F]]
 [[Category: Ferraroni, M]]

3nw4

From Proteopedia

Revision as of 08:08, 4 November 2020

Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with gentisate

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

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