View source for 1eg9


==NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.==
<StructureSection load='1eg9' size='340' side='right'caption='[[1eg9]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1eg9]] is a 2 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=1EG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EG9 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
<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>, <scene name='pdbligand=IND:INDOLE'>IND</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1eg9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg9 OCA], [https://pdbe.org/1eg9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eg9 RCSB], [https://www.ebi.ac.uk/pdbsum/1eg9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eg9 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/eg/1eg9_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=1eg9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products.

Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding.,Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S J Mol Biol. 2000 Feb 18;296(2):701-12. PMID:10669618<ref>PMID:10669618</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1eg9" style="background-color:#fffaf0;"></div>

==See Also==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Carredano E]]
[[Category: Choudhury D]]
[[Category: Eklund H]]
[[Category: Gibson DT]]
[[Category: Karlsson A]]
[[Category: Kauppi B]]
[[Category: Lee K]]
[[Category: Parales JV]]
[[Category: Parales RE]]
[[Category: Ramaswamy S]]