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| | <StructureSection load='3hpv' size='340' side='right'caption='[[3hpv]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3hpv' size='340' side='right'caption='[[3hpv]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [https://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=3HPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3hpv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_alkylphenolica Pseudomonas alkylphenolica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HPV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Pseudomonas sp. KL28 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=237609 "Pseudomonas alkylphenolia" Veeranagouda et al. 2009])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catechol_2,3-dioxygenase Catechol 2,3-dioxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.2 1.13.11.2] </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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [https://pdbe.org/3hpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [https://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv 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=3hpv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpv OCA], [https://pdbe.org/3hpv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hpv RCSB], [https://www.ebi.ac.uk/pdbsum/3hpv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpv ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q7WYF5_9PSED Q7WYF5_9PSED] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pseudomonas alkylphenolia veeranagouda et al. 2009]] | |
| - | [[Category: Catechol 2,3-dioxygenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cho, J H]] | + | [[Category: Pseudomonas alkylphenolica]] |
| - | [[Category: Rhee, S]] | + | [[Category: Cho J-H]] |
| - | [[Category: Aromatic hydrocarbons catabolism]] | + | [[Category: Rhee S]] |
| - | [[Category: Dioxygenase]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Repeated motif]]
| + | |
| Structural highlights
Function
Q7WYF5_9PSED
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 PubMed
LapB 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 Also
References
- ↑ Cho JH, Jung DK, Lee K, Rhee S. Crystal structure and functional analysis of the extradiol dioxygenase LapB from a long-chain alkylphenol degradation pathway in Pseudomonas. J Biol Chem. 2009 Dec 4;284(49):34321-30. Epub 2009 Oct 14. PMID:19828456 doi:http://dx.doi.org/10.1074/jbc.M109.031054
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