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1ndo

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[[Image:1ndo.gif|left|200px]]<br />
 
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<applet load="1ndo" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ndo, resolution 2.25&Aring;" />
 
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'''NAPTHALENE 1,2-DIOXYGENASE'''<br />
 
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==Overview==
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==NAPHTHALENE 1,2-DIOXYGENASE==
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BACKGROUND: Pseudomonas sp. NCIB 9816-4 utilizes a multicomponent enzyme, system to oxidize naphthalene to, (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. The enzyme component, catalyzing this reaction, naphthalene 1,2-dioxygenase (NDO), belongs to a, family of aromatic-ring-hydroxylating dioxygenases that oxidize aromatic, hydrocarbons and related compounds to cis-arene diols. These enzymes, utilize a mononuclear non-heme iron center to catalyze the addition of, dioxygen to their respective substrates. The present study was conducted, to provide essential structural information necessary for elucidating the, mechanism of action of NDO. RESULTS: The three-dimensional structure of, NDO has been determined at 2.25 A resolution. The molecule is an alpha 3, beta 3 hexamer. The alpha subunit has a beta-sheet domain that contains a, Rieske [2Fe-2S] center and a catalytic domain that has a novel fold, dominated by an antiparallel nine-stranded beta-pleated sheet against, which helices pack. The active site contains a non-heme ferrous ion, coordinated by His208, His213, Asp362 (bidentate) and a water molecule., Asn201 is positioned further away, 3.75 A, at the missing axial position, of an octahedron. In the Rieske [2Fe-2S] center, one iron is coordinated, by Cys81 and Cys101 and the other by His83 and His104. CONCLUSIONS: The, domain structure and iron coordination of the Rieske domain is very, similar to that of the cytochrome bc1 domain. The active-site iron center, of one of the alpha subunits is directly connected by hydrogen bonds, through a single amino acid, Asp205, to the Rieske [2Fe-2S] center in a, neighboring alpha subunit. This is likely to be the main route for, electron transfer.
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<StructureSection load='1ndo' size='340' side='right'caption='[[1ndo]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ndo]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDO FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ndo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndo OCA], [https://pdbe.org/1ndo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndo RCSB], [https://www.ebi.ac.uk/pdbsum/1ndo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndo ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDOB_PSEPU NDOB_PSEPU] Component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyzes the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndo_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ndo ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NDO is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with FE and FES as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Naphthalene_1,2-dioxygenase Naphthalene 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.12 1.14.12.12] Structure known Active Sites: MO1, MO2, MO3, RK1, RK2 and RK3. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NDO OCA].
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase., Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S, Structure. 1998 May 15;6(5):571-86. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9634695 9634695]
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[[Category: Large Structures]]
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[[Category: Naphthalene 1,2-dioxygenase]]
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[[Category: Protein complex]]
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[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
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[[Category: Carredano, E.]]
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[[Category: Carredano E]]
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[[Category: Kauppi, B.]]
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[[Category: Kauppi B]]
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[[Category: Ramaswamy, S.]]
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[[Category: Ramaswamy S]]
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[[Category: FE]]
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[[Category: FES]]
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[[Category: non-heme iron dioxygenase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 13:44:22 2007''
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NAPHTHALENE 1,2-DIOXYGENASE

PDB ID 1ndo

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