4nbb: Difference between revisions
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==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase== | ==Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase== | ||
<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution|resolution]] 2.05Å' scene=''> | <StructureSection load='4nbb' size='340' side='right'caption='[[4nbb]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure with sequence from [ | <table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Janthinobacterium_sp._J3 Janthinobacterium sp. J3] and [https://en.wikipedia.org/wiki/Pseudomonas_resinovorans Pseudomonas resinovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene | </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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9CA:9H-CARBAZOLE'>9CA</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [https://pdbe.org/4nbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [https://www.ebi.ac.uk/pdbsum/4nbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbb ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/Q84II6_JANS3 Q84II6_JANS3] | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 19: | Line 18: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4nbb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Janthinobacterium sp. J3]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pseudomonas resinovorans]] | ||
[[Category: Ashikawa | [[Category: Ashikawa Y]] | ||
[[Category: Inoue | [[Category: Inoue K]] | ||
[[Category: Nojiri | [[Category: Nojiri H]] | ||
[[Category: Usami | [[Category: Usami Y]] | ||
Latest revision as of 17:47, 8 November 2023
Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenaseCarbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase
Structural highlights
FunctionPublication Abstract from PubMedCarbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15 degrees , 25 degrees , and 25 degrees , respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates. Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Non-heme Iron Oxygenase, Carbazole 1,9a-Dioxygenase.,Inoue K, Usami Y, Ashikawa Y, Noguchi H, Umeda T, Yamagami-Ashikawa A, Horisaki T, Uchimura H, Terada T, Nakamura S, Shimizu K, Habe H, Yamane H, Fujimoto Z, Nojiri H Appl Environ Microbiol. 2014 Feb 28. PMID:24584240[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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