4jek
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4jek]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._IGTS8 Rhodococcus sp. IGTS8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JEK FirstGlance]. <br> | <table><tr><td colspan='2'>[[4jek]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_sp._IGTS8 Rhodococcus sp. IGTS8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JEK FirstGlance]. <br> | ||
| - | </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=4jek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jek OCA], [https://pdbe.org/4jek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jek RCSB], [https://www.ebi.ac.uk/pdbsum/4jek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jek ProSAT]</span></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]] 2.4Å</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=4jek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jek OCA], [https://pdbe.org/4jek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jek RCSB], [https://www.ebi.ac.uk/pdbsum/4jek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jek ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/DSZC_RHOSG DSZC_RHOSG] Catalyzes the first step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Sulfur dioxygenase which converts DBT to DBT-sulfone (DBTO2 or DBT 5,5-dioxide) in a stepwise manner. In (PubMed:7961424) DBTO (dibenzothiophene-5-oxide) was reported not to be a substrate, in (PubMed:7574582, PubMed:9634856, PubMed:8824615 and PubMed:9308179) it is reported to be a substrate (PubMed:7961424, PubMed:7574582, PubMed:9634856, PubMed:8824615, PubMed:9308179). Can also use benzyl sulfide and benzyl sulfoxide as substrates, although benzyl sulfoxide is a poor substrate (PubMed:8824615). The pathway substrate specificity has been augmented using mutagenesis, however no mutations allowed use of alkylated thiophenes (PubMed:11823208).<ref>PMID:11823208</ref> <ref>PMID:7574582</ref> <ref>PMID:7961424</ref> <ref>PMID:8824615</ref> <ref>PMID:9308179</ref> <ref>PMID:9634856</ref> | [https://www.uniprot.org/uniprot/DSZC_RHOSG DSZC_RHOSG] Catalyzes the first step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Sulfur dioxygenase which converts DBT to DBT-sulfone (DBTO2 or DBT 5,5-dioxide) in a stepwise manner. In (PubMed:7961424) DBTO (dibenzothiophene-5-oxide) was reported not to be a substrate, in (PubMed:7574582, PubMed:9634856, PubMed:8824615 and PubMed:9308179) it is reported to be a substrate (PubMed:7961424, PubMed:7574582, PubMed:9634856, PubMed:8824615, PubMed:9308179). Can also use benzyl sulfide and benzyl sulfoxide as substrates, although benzyl sulfoxide is a poor substrate (PubMed:8824615). The pathway substrate specificity has been augmented using mutagenesis, however no mutations allowed use of alkylated thiophenes (PubMed:11823208).<ref>PMID:11823208</ref> <ref>PMID:7574582</ref> <ref>PMID:7961424</ref> <ref>PMID:8824615</ref> <ref>PMID:9308179</ref> <ref>PMID:9634856</ref> | ||
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| - | == Publication Abstract from PubMed == | ||
| - | Dibenzothiophene (DBT) and its derivatives are typical sulfur compounds found in fossil fuels. These compounds show resistance to the hydrodesulfurization treatment that is commonly used in industry. Dibenzothiophene monooxygenase (DszC) is responsible for the oxidation of DBT, which is the first and the rate-limiting step in the DBT enzymatic desulfurization 4S pathway. In this study, the crystal structure of DszC from Rhodococcus erythropolis DS-3 is reported. The crystal of native DszC belonged to space group P1, with unit-cell parameters a = 96.16, b = 96.27, c = 98.56 A, alpha = 81.03, beta = 67.57, gamma = 85.84 degrees . To determine the phase, SAD X-ray diffraction data were collected from a SeMet-derivative DszC crystal, which also belonged to space group P1, with unit-cell parameters a = 95.379, b = 95.167, c = 94.891 A, alpha = 87.046, beta = 70.536, gamma = 79.738 degrees . Further structural analysis of DszC is in progress. | ||
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| - | Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis.,Duan X, Zhang L, Zhou D, Ji K, Ma T, Shui W, Li G, Li X Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Jun;69(Pt 6):597-601. doi:, 10.1107/S1744309113011172. Epub 2013 May 23. PMID:23722833<ref>PMID:23722833</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4jek" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Structure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis
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