1ndo: Difference between revisions

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{{Seed}}
[[Image:1ndo.png|left|200px]]


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==NAPHTHALENE 1,2-DIOXYGENASE==
The line below this paragraph, containing "STRUCTURE_1ndo", creates the "Structure Box" on the page.
<StructureSection load='1ndo' size='340' side='right'caption='[[1ndo]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_1ndo|  PDB=1ndo  |  SCENE=  }}
<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>
</table>
== Function ==
[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.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndo_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===NAPTHALENE 1,2-DIOXYGENASE===
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:9634695<ref>PMID:9634695</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ndo" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_9634695}}, adds the Publication Abstract to the page
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 9634695 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_9634695}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1NDO is a [[Protein complex]] structure of sequences from [http://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].
 
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/9634695 9634695]
[[Category: Naphthalene 1,2-dioxygenase]]
[[Category: Protein complex]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
[[Category: Carredano, E.]]
[[Category: Carredano E]]
[[Category: Kauppi, B.]]
[[Category: Kauppi B]]
[[Category: Ramaswamy, S.]]
[[Category: Ramaswamy S]]
[[Category: Non-heme iron dioxygenase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:43:01 2008''
Retrieved from "https://proteopedia.org/1ndo"