2wl9: Difference between revisions
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<StructureSection load='2wl9' size='340' side='right'caption='[[2wl9]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='2wl9' size='340' side='right'caption='[[2wl9]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2wl9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp. | <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='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='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> | <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> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q6REQ5_9NOCA Q6REQ5_9NOCA] | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Rhodococcus sp. | [[Category: Rhodococcus sp. DK17]] | ||
[[Category: Cho | [[Category: Cho HJ]] | ||
[[Category: Kang | [[Category: Kang BS]] | ||
[[Category: Kim | [[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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