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== | |||
<StructureSection load='4nbb' size='340' side='right' caption='[[4nbb]], [[Resolution|resolution]] 2.05Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4nbb]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_14235 Atcc 14235] and [http://en.wikipedia.org/wiki/Jans3 Jans3]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NBB FirstGlance]. <br> | |||
==Function== | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nb8|4nb8]], [[4nb9|4nb9]], [[4nba|4nba]], [[4nbc|4nbc]], [[4nbd|4nbd]], [[4nbe|4nbe]], [[4nbf|4nbf]], [[4nbg|4nbg]], [[4nbh|4nbh]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">carAa ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=213804 JANS3]), carAc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53412 ATCC 14235])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbazole_1,9a-dioxygenase Carbazole 1,9a-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.22 1.14.12.22] </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=4nbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nbb RCSB], [http://www.ebi.ac.uk/pdbsum/4nbb PDBsum]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref> | [[http://www.uniprot.org/uniprot/CARAC_PSERE CARAC_PSERE]] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.<ref>PMID:9244274</ref> <ref>PMID:12450807</ref> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Carbazole 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<ref>PMID:24584240</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Atcc 14235]] | |||
[[Category: Carbazole 1,9a-dioxygenase]] | [[Category: Carbazole 1,9a-dioxygenase]] | ||
[[Category: Ashikawa, Y | [[Category: Jans3]] | ||
[[Category: Inoue, K | [[Category: Ashikawa, Y]] | ||
[[Category: Nojiri, H | [[Category: Inoue, K]] | ||
[[Category: Usami, Y | [[Category: Nojiri, H]] | ||
[[Category: Usami, Y]] | |||
[[Category: 9a-dioxygenase]] | [[Category: 9a-dioxygenase]] | ||
[[Category: Carbazole 1]] | [[Category: Carbazole 1]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
[[Category: Rieske non-heme iron oxygenase]] | [[Category: Rieske non-heme iron oxygenase]] | ||
Revision as of 00:20, 26 December 2014
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
Function[CARAC_PSERE] Part of the multicomponent carbazole 1,9a-dioxygenase (CARDO), that converts carbazole (CAR) into 2-aminobiphenyl-2,3-diol. Acts as a mediator in the electron transfer from CarAd to CarAa.[1] [2] Publication 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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