3gce: Difference between revisions

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{{Seed}}
[[Image:3gce.jpg|left|200px]]


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==Ferredoxin of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177==
The line below this paragraph, containing "STRUCTURE_3gce", creates the "Structure Box" on the page.
<StructureSection load='3gce' size='340' side='right'caption='[[3gce]], [[Resolution|resolution]] 2.00&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'>[[3gce]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Nocardioides_aromaticivorans Nocardioides aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GCE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GCE 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&#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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
{{STRUCTURE_3gce|  PDB=3gce  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gce OCA], [https://pdbe.org/3gce PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gce RCSB], [https://www.ebi.ac.uk/pdbsum/3gce PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gce ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q2HWH6_9ACTN Q2HWH6_9ACTN]
== 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/gc/3gce_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=3gce ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Carbazole 1,9a-dioxygenase (CARDO) consists of terminal oxygenase (Oxy), ferredoxin (Fd), and ferredoxin reductase (Red) components and is a member of the Rieske nonheme iron oxygenases. Rieske nonheme iron oxygenases are divided into five subclasses (IA, IB, IIA, IIB, and III) based on the number of constituents and the nature of their redox centers. Each component of a class IIB CARDO from Nocardioides aromaticivorans IC177 was purified, and the interchangeability of the electron transfer reactions with each component from the class III CARDOs was investigated. Despite the fact that the Fds of both classes are Rieske-type, strict specificities between the Oxy and Fd components were observed. On the other hand, the Fd and Red components were interchangeable, even though the Red components differ in cofactor composition; the class IIB Red contains flavin-adenine-dinucleotide (FAD)- and NADH-binding domains, whereas the class III Red has a chloroplast-type [2Fe-2S] cluster in addition to the FAD- and NADH-binding domains. The crystal structures of the class IIB Oxy and Fd components were compared to the previously reported Fd:Oxy complex structure of class III CARDO. This comparison suggested residues in common between class IIB and class III CARDOs that are important for interactions between Fd and Oxy. In the class IIB CARDOs, these included His75 and Glu71 in Fd and Lys20 and Glu357 in Oxy for electrostatic interactions, and Phe74 and Pro90 in Fd and Trp21, Leu359, and Val367 in Oxy for hydrophobic interactions. The residues that formed the interacting surface but were not conserved between classes were thought to be necessary to form the appropriate geometry and to determine electron transfer specificity between Fd and Oxy.


===Ferredoxin of carbazole 1,9a-dioxygenase from Nocardioides aromaticivorans IC177===
Specific Interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase.,Inoue K, Ashikawa Y, Umeda T, Abo M, Katsuki J, Usami Y, Noguchi H, Fujimoto Z, Terada T, Yamane H, Nojiri H J Mol Biol. 2009 Sep 18;392(2):436-51. Epub 2009 Jul 17. PMID:19616558<ref>PMID:19616558</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gce" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19616558}}, adds the Publication Abstract to the page
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19616558 is the PubMed ID number.
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
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== References ==
{{ABSTRACT_PUBMED_19616558}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
3GCE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Nocardioides_aromaticivorans Nocardioides aromaticivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GCE OCA].
[[Category: Large Structures]]
 
==Reference==
<ref group="xtra">PMID:19616558</ref><references group="xtra"/>
[[Category: Nocardioides aromaticivorans]]
[[Category: Nocardioides aromaticivorans]]
[[Category: Inoue, K.]]
[[Category: Inoue K]]
[[Category: Nojiri, H.]]
[[Category: Nojiri H]]
[[Category: 2fe-2]]
[[Category: Carbazole]]
[[Category: Dioxygenase]]
[[Category: Electron transfer]]
[[Category: Oxidoreductase]]
[[Category: Rieske ferredoxin]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 09:01:47 2009''
Retrieved from "https://proteopedia.org/3gce"