4jek

From Proteopedia

(Difference between revisions)

Revision as of 11:09, 24 November 2022

Structure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis

Structural highlights

4jek is a 8 chain structure with sequence from Rhodococcus sp. IGTS8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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.

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Arensdorf JJ, Loomis AK, DiGrazia PM, Monticello DJ, Pienkos PT. Chemostat approach for the directed evolution of biodesulfurization gain-of-function mutants. Appl Environ Microbiol. 2002 Feb;68(2):691-8. doi: 10.1128/AEM.68.2.691-698.2002. PMID:11823208 doi:http://dx.doi.org/10.1128/AEM.68.2.691-698.2002
↑ Piddington CS, Kovacevich BR, Rambosek J. Sequence and molecular characterization of a DNA region encoding the dibenzothiophene desulfurization operon of Rhodococcus sp. strain IGTS8. Appl Environ Microbiol. 1995 Feb;61(2):468-75. PMID:7574582
↑ Denome SA, Oldfield C, Nash LJ, Young KD. Characterization of the desulfurization genes from Rhodococcus sp. strain IGTS8. J Bacteriol. 1994 Nov;176(21):6707-16. PMID:7961424
↑ Lei B, Tu SC. Gene overexpression, purification, and identification of a desulfurization enzyme from Rhodococcus sp. strain IGTS8 as a sulfide/sulfoxide monooxygenase. J Bacteriol. 1996 Oct;178(19):5699-705. doi: 10.1128/jb.178.19.5699-5705.1996. PMID:8824615 doi:http://dx.doi.org/10.1128/jb.178.19.5699-5705.1996
↑ Oldfield C, Pogrebinsky O, Simmonds J, Olson ES, Kulpa CF. Elucidation of the metabolic pathway for dibenzothiophene desulphurization by Rhodococcus sp. strain IGTS8 (ATCC 53968). Microbiology (Reading). 1997 Sep;143 ( Pt 9):2961-2973. doi: , 10.1099/00221287-143-9-2961. PMID:9308179 doi:http://dx.doi.org/10.1099/00221287-143-9-2961
↑ Gray KA, Pogrebinsky OS, Mrachko GT, Xi L, Monticello DJ, Squires CH. Molecular mechanisms of biocatalytic desulfurization of fossil fuels. Nat Biotechnol. 1996 Dec;14(13):1705-9. doi: 10.1038/nbt1296-1705. PMID:9634856 doi:http://dx.doi.org/10.1038/nbt1296-1705
↑ Duan X, Zhang L, Zhou D, Ji K, Ma T, Shui W, Li G, Li X. Crystallization and preliminary structural analysis of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis. 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 doi:10.1107/S1744309113011172

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4jek"

@@ Line 1: / Line 1: @@
 ==Structure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis==
-<StructureSection load='4jek' size='340' side='right' caption='[[4jek]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='4jek' size='340' side='right'caption='[[4jek]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4jek]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhosg Rhosg]. 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 [http://oca.weizmann.ac.il/oca-docs/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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">soxC, dszC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>
+</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jek OCA], [http://pdbe.org/4jek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jek RCSB], [http://www.ebi.ac.uk/pdbsum/4jek PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jek ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SOXC_RHOSG SOXC_RHOSG]] Part of a pathway to remove 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).
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Rhosg]]
+[[Category: Large Structures]]
-[[Category: Duan, X L]]
+[[Category: Rhodococcus sp. IGTS8]]
-[[Category: Li, X]]
+[[Category: Duan XL]]
-[[Category: Zhang, L]]
+[[Category: Li X]]
-[[Category: Zhou, D M]]
+[[Category: Zhang L]]
-[[Category: Dibenzothiophene desulfurization enzyme c]]
+[[Category: Zhou DM]]
-[[Category: Oxidoreductase]]

4jek

From Proteopedia

Revision as of 11:09, 24 November 2022

Structure of dibenzothiophene monooxygenase (DszC) from Rhodococcus erythropolis

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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