2wl9: Difference between revisions
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==Crystal structure of catechol 2,3-dioxygenase== | |||
<StructureSection load='2wl9' size='340' side='right'caption='[[2wl9]], [[Resolution|resolution]] 1.90Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2wl9]] 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=2WL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WL9 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]] 1.9Å</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MBD:3-METHYLCATECHOL'>MBD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2wl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wl9 OCA], [https://pdbe.org/2wl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wl9 RCSB], [https://www.ebi.ac.uk/pdbsum/2wl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wl9 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/2wl9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2wl9 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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2wl9" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
[[ | *[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Rhodococcus sp. DK17]] | ||
[[Category: | [[Category: Cho HJ]] | ||
[[Category: | [[Category: Kang BS]] | ||
[[Category: Kim KJ]] | |||
Latest revision as of 19:01, 13 December 2023
Crystal structure of catechol 2,3-dioxygenaseCrystal structure of catechol 2,3-dioxygenase
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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