1ww9

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(Difference between revisions)

Revision as of 01:34, 12 September 2015

Crystal structure of the terminal oxygenase component of carbazole 1,9a-dioxygenase, a non-heme iron oxygenase system catalyzing the novel angular dioxygenation for carbazole and dioxin

Structural highlights

1ww9 is a 1 chain structure with sequence from Jans3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Carbazole 1,9a-dioxygenase (CARDO) catalyzes the dihydroxylation of carbazole by angular position (C9a) carbon bonding to the imino nitrogen and its adjacent C1 carbon. This reaction is an initial degradation reaction of the carbazole degradation pathway by various bacterial strains. Only a limited number of Rieske non-heme iron oxygenase systems (ROSs) can catalyze this novel reaction, termed angular dioxygenation. Angular dioxygenation is also involved in the degradation pathways of carbazole-related compounds, dioxin, and CARDO can catalyze the angular dioxygenation for dioxin. CARDO consists of a terminal oxygenase component (CARDO-O), and the electron transport components, ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R). CARDO-O has a homotrimeric structure, and governs the substrate specificity of CARDO. Here, we have determined the crystal structure of CARDO-O of Janthinobacterium sp. strain J3 at a resolution of 1.95A. The alpha3 trimeric overall structure of the CARDO-O molecule roughly corresponds to the alpha3 partial structures of other terminal oxygenase components of ROSs that have the alpha3beta3 configuration. The CARDO-O structure is a first example of the terminal oxygenase components of ROSs that have the alpha3 configuration, and revealed the presence of the specific loops that interact with a neighboring subunit, which is proposed to be indispensable for stable alpha3 interactions without structural beta subunits. The shape of the substrate-binding pocket of CARDO-O is markedly different from those of other oxygenase components involved in naphthalene and biphenyl degradation pathways. Docking simulations suggested that carbazole binds to the substrate-binding pocket in a manner suitable for catalysis of angular dioxygenation.

Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase.,Nojiri H, Ashikawa Y, Noguchi H, Nam JW, Urata M, Fujimoto Z, Uchimura H, Terada T, Nakamura S, Shimizu K, Yoshida T, Habe H, Omori T J Mol Biol. 2005 Aug 12;351(2):355-70. PMID:16005887^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nojiri H, Ashikawa Y, Noguchi H, Nam JW, Urata M, Fujimoto Z, Uchimura H, Terada T, Nakamura S, Shimizu K, Yoshida T, Habe H, Omori T. Structure of the terminal oxygenase component of angular dioxygenase, carbazole 1,9a-dioxygenase. J Mol Biol. 2005 Aug 12;351(2):355-70. PMID:16005887 doi:10.1016/j.jmb.2005.05.059

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ww9"

@@ Line 2: / Line 2: @@
 <StructureSection load='1ww9' size='340' side='right' caption='[[1ww9]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ww9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Janthinobacterium_sp._j3 Janthinobacterium sp. j3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WW9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ww9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Jans3 Jans3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WW9 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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></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=1ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ww9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ww9 PDBsum]</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=1ww9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ww9 OCA], [http://pdbe.org/1ww9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ww9 RCSB], [http://www.ebi.ac.uk/pdbsum/1ww9 PDBsum]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 24: / Line 24: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ww9" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Janthinobacterium sp. j3]]
+[[Category: Jans3]]
 [[Category: Ashikawa, Y]]
 [[Category: Fujimoto, Z]]

1ww9

From Proteopedia

Revision as of 01:34, 12 September 2015

Crystal structure of the terminal oxygenase component of carbazole 1,9a-dioxygenase, a non-heme iron oxygenase system catalyzing the novel angular dioxygenation for carbazole and dioxin

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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