1eg9: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='1eg9' size='340' side='right'caption='[[1eg9]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='1eg9' size='340' side='right'caption='[[1eg9]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1eg9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. 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>
<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='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>
</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Naphthalene_1,2-dioxygenase Naphthalene 1,2-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.12 1.14.12.12] </span></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>
<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>
</table>
== Function ==
== 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. [[https://www.uniprot.org/uniprot/NDOC_PSEPU NDOC_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. The beta subunit may be responsible for the substrate specificity of the enzyme.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 20: Line 20:
</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].
</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="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>
</div>
<div class="pdbe-citations 1eg9" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus fluorescens putidus flugge 1886]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Naphthalene 1,2-dioxygenase]]
[[Category: Pseudomonas putida]]
[[Category: Carredano, E]]
[[Category: Carredano E]]
[[Category: Choudhury, D]]
[[Category: Choudhury D]]
[[Category: Eklund, H]]
[[Category: Eklund H]]
[[Category: Gibson, D T]]
[[Category: Gibson DT]]
[[Category: Karlsson, A]]
[[Category: Karlsson A]]
[[Category: Kauppi, B]]
[[Category: Kauppi B]]
[[Category: Lee, K]]
[[Category: Lee K]]
[[Category: Parales, J V]]
[[Category: Parales JV]]
[[Category: Parales, R E]]
[[Category: Parales RE]]
[[Category: Ramaswamy, S]]
[[Category: Ramaswamy S]]
[[Category: Enzyme-substrate complex]]
[[Category: Non-heme iron dioxygenase]]
[[Category: Oxidoreductase]]

Latest revision as of 10:02, 7 February 2024

NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.

Structural highlights

1eg9 is a 2 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

See Also

1eg9, resolution 1.60Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1eg9&oldid=4042540"