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| | ==Crystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1== | | ==Crystal structure of FMN-bound DszC from Rhodococcus erythropolis D-1== |
| - | <StructureSection load='3x0y' size='340' side='right' caption='[[3x0y]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3x0y' size='340' side='right'caption='[[3x0y]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3x0y]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"mycobacterium_erythropolis"_gray_and_thornton_1928 "mycobacterium erythropolis" gray and thornton 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X0Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3x0y]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_erythropolis Rhodococcus erythropolis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X0Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3x0x|3x0x]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dszC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1833 "Mycobacterium erythropolis" Gray and Thornton 1928])</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=3x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x0y OCA], [https://pdbe.org/3x0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x0y RCSB], [https://www.ebi.ac.uk/pdbsum/3x0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x0y 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=3x0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x0y OCA], [http://pdbe.org/3x0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3x0y RCSB], [http://www.ebi.ac.uk/pdbsum/3x0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3x0y ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DSZC1_RHOER DSZC1_RHOER] 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 (PubMed:11229908, Ref.2). Also acts on thioxanthen-9-one and 4,6-dimethyl DBT and 2,8-dimethyl DBT (Ref.2).<ref>PMID:11229908</ref> <ref>PMID:25627402</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Mycobacterium erythropolis gray and thornton 1928]] | + | [[Category: Large Structures]] |
| - | [[Category: Guan, L J]] | + | [[Category: Rhodococcus erythropolis]] |
| - | [[Category: Lee, W C]] | + | [[Category: Guan LJ]] |
| - | [[Category: Ohtsuka, J]] | + | [[Category: Lee WC]] |
| - | [[Category: Tanokura, M]] | + | [[Category: Ohtsuka J]] |
| - | [[Category: Wang, S P]] | + | [[Category: Tanokura M]] |
| - | [[Category: Acyl-coa dehydrogenase domain]]
| + | [[Category: Wang SP]] |
| - | [[Category: Dbt monooxygenase]]
| + | |
| - | [[Category: Desulfurization]]
| + | |
| - | [[Category: Fmn-dependent]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
DSZC1_RHOER 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 (PubMed:11229908, Ref.2). Also acts on thioxanthen-9-one and 4,6-dimethyl DBT and 2,8-dimethyl DBT (Ref.2).[1] [2]
Publication Abstract from PubMed
The release of SO2 from petroleum products derived from crude oil, which contains sulfur compounds such as dibenzothiophene (DBT), leads to air pollution. The '4S' metabolic pathway catalyzes the sequential conversion of DBT to 2-hydroxybiphenyl via three enzymes encoded by the dsz operon in several bacterial species. DszC (DBT monooxygenase), from Rhodococcus erythropolis D-1 is involved in the first two steps of the '4S' pathway. Here, we determined the first crystal structure of FMN-bound DszC, and found that two distinct conformations occur in the loop region (residues 131-142) adjacent to the active site. On the basis of the DszC-FMN structure and the previously reported apo structures of DszC homologs, the binding site for DBT and DBT sulfoxide is proposed. DATABASE: The atomic coordinates and structure factors for apo-DszC (PDB code: 3X0X) and DszC-FMN (PDB code: 3X0Y) have been deposited in the Protein Data Bank (http://www.rcsb.org).
Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1.,Guan LJ, Lee WC, Wang S, Ohshiro T, Izumi Y, Ohtsuka J, Tanokura M FEBS J. 2015 Jan 28. doi: 10.1111/febs.13216. PMID:25627402[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Matsubara T, Ohshiro T, Nishina Y, Izumi Y. Purification, characterization, and overexpression of flavin reductase involved in dibenzothiophene desulfurization by Rhodococcus erythropolis D-1. Appl Environ Microbiol. 2001 Mar;67(3):1179-84. PMID:11229908 doi:10.1128/AEM.67.3.1179-1184
- ↑ Guan LJ, Lee WC, Wang S, Ohshiro T, Izumi Y, Ohtsuka J, Tanokura M. Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1. FEBS J. 2015 Jan 28. doi: 10.1111/febs.13216. PMID:25627402 doi:http://dx.doi.org/10.1111/febs.13216
- ↑ Guan LJ, Lee WC, Wang S, Ohshiro T, Izumi Y, Ohtsuka J, Tanokura M. Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1. FEBS J. 2015 Jan 28. doi: 10.1111/febs.13216. PMID:25627402 doi:http://dx.doi.org/10.1111/febs.13216
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