3hq0: Difference between revisions
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==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in complex with a product== | ==Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in complex with a product== | ||
<StructureSection load='3hq0' size='340' side='right' caption='[[3hq0]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3hq0' size='340' side='right'caption='[[3hq0]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3hq0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HQ0 FirstGlance]. <br> | <table><tr><td colspan='2'>[[3hq0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pseudomonas_alkylphenolia"_veeranagouda_et_al._2009 "pseudomonas alkylphenolia" veeranagouda et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HQ0 FirstGlance]. <br> | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hq/3hq0_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hq/3hq0_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3hq0" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3hq0" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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[[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]] | [[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]] | ||
[[Category: Catechol 2,3-dioxygenase]] | [[Category: Catechol 2,3-dioxygenase]] | ||
[[Category: Large Structures]] | |||
[[Category: Cho, J H]] | [[Category: Cho, J H]] | ||
[[Category: Rhee, S]] | [[Category: Rhee, S]] | ||
Revision as of 09:38, 7 August 2019
Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in complex with a productCrystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in complex with a product
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedLapB is a non-heme Fe(II)-dependent 2,3-dioxygenase that catalyzes the second step of a long-chain alkylphenol (lap) degradation pathway in Pseudomonas sp. KL28 and belongs to the superfamily of type I extradiol dioxygenases. In this study, the crystal structures of substrate-free LapB and its complexes with a substrate or product were determined, along with a functional analysis of the active site residues. Structural features of the homotetramer are similar to those of other type I extradiol dioxygenases. In particular, the active site is located in the C-domain of each monomer, with a 2-His-1-carboxylate motif as the first coordination shell to iron ion. A comparison of three different structures in the catalytic cycle indicated catalysis-related local conformational changes in the active site. Specifically, the active site loop containing His-248 exhibits positional changes upon binding of the substrate and establishes a hydrogen-bonding network with Tyr-257, which is near the hydroxyl group of the substrate. Kinetic analysis of the mutant enzymes H248A, H248N, and Y257F showed that these three mutant enzymes are inactive, suggesting that this hydrogen-bonding network plays a crucial role in catalysis by deprotonating the incoming substrate and leaving it in a monoanionic state. Additional functional analysis of His-201, by using H201A and H201N mutants, near the dioxygen-binding site also supports its role as base and acid catalyst in the late stage of catalysis. We also noticed a disordered-to-ordered structural transition in the C-terminal region, resulting in the opening or closing of the active site. These results provide detailed insights into the structural and functional features of an extradiol dioxygenase that can accommodate a wide range of alkylcatechols. Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas.,Cho JH, Jung DK, Lee K, Rhee S J Biol Chem. 2009 Dec 4;284(49):34321-30. Epub 2009 Oct 14. PMID:19828456[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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