2wl3: Difference between revisions

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{{Seed}}
[[Image:2wl3.png|left|200px]]


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==crystal structure of catechol 2,3-dioxygenase==
The line below this paragraph, containing "STRUCTURE_2wl3", creates the "Structure Box" on the page.
<StructureSection load='2wl3' size='340' side='right'caption='[[2wl3]], [[Resolution|resolution]] 2.20&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'>[[2wl3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._DK17 Rhodococcus sp. DK17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WL3 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]] 2.2&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_2wl3|  PDB=2wl3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wl3 OCA], [https://pdbe.org/2wl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wl3 RCSB], [https://www.ebi.ac.uk/pdbsum/2wl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wl3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q6REQ5_9NOCA Q6REQ5_9NOCA]
== 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/wl/2wl3_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=2wl3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A meta-cleavage pathway for the aerobic degradation of aromatic hydrocarbons is catalyzed by extradiol dioxygenases via a two-step mechanism: catechol substrate binding and dioxygen incorporation. The binding of substrate triggers the release of water, thereby opening a coordination site for molecular oxygen. The crystal structures of AkbC, a type I extradiol dioxygenase, and the enzyme-substrate (3-methylcatechol) complex revealed the substrate-binding process of extradiol dioxygenase. AkbC is composed of an N-domain and an active C-domain, which contains iron coordinated by a 2-His-1-carboxylate facial triad motif. The C-domain includes a beta-hairpin structure and a C-terminal tail. In substrate-bound AkbC, 3-methylcatechol interacts with the iron via a single hydroxyl group, which represents an intermediate stage in the substrate-binding process. Structure-based mutagenesis revealed that the C-terminal tail and beta-hairpin form part of the substrate-binding pocket that is responsible for substrate specificity by blocking substrate entry. Once a substrate enters the active site, these structural elements also play a role in the correct positioning of the substrate. Based on the results presented here, a putative substrate-binding mechanism is proposed.


===CRYSTAL STRUCTURE OF CATECHOL 2,3-DIOXYGENASE===
Substrate-binding mechanism of a type I extradiol dioxygenase.,Cho HJ, Kim K, Sohn SY, Cho HY, Kim KJ, Kim MH, Kim D, Kim E, Kang BS J Biol Chem. 2010 Sep 1. PMID:20810655<ref>PMID:20810655</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2wl3" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_20810655}}, adds the Publication Abstract to the page
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 20810655 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20810655}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2WL3 is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Rhodococcus_sp._dk17 Rhodococcus sp. dk17]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WL3 OCA].
[[Category: Rhodococcus sp. DK17]]
 
[[Category: Cho HJ]]
==Reference==
[[Category: Kang BS]]
<ref group="xtra">PMID:20810655</ref><references group="xtra"/>
[[Category: Kim KJ]]
[[Category: Rhodococcus sp. dk17]]
[[Category: Cho, H J.]]
[[Category: Kang, B S.]]
[[Category: Kim, K J.]]
[[Category: Akbc]]
[[Category: Aromatic hydrocarbons catabolism]]
[[Category: Oxidoreductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 15 10:16:05 2010''

Latest revision as of 09:34, 6 November 2024

crystal structure of catechol 2,3-dioxygenase

2wl3, resolution 2.20Å

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