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| | ==Crystal structure of DSZB C27S mutant in complex with biphenyl-2-sulfinic acid== | | ==Crystal structure of DSZB C27S mutant in complex with biphenyl-2-sulfinic acid== |
| - | <StructureSection load='2de4' size='340' side='right' caption='[[2de4]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='2de4' size='340' side='right'caption='[[2de4]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2de4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DE4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2de4]] is a 2 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=2DE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE4 FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BPS:1,1-BIPHENYL-2-SULFINIC+ACID'>BPS</scene><br> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2de2|2de2]], [[2de3|2de3]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=BPS:1,1-BIPHENYL-2-SULFINIC+ACID'>BPS</scene></td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DSZB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1831 Rhodococcus sp.])</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=2de4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de4 OCA], [https://pdbe.org/2de4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de4 RCSB], [https://www.ebi.ac.uk/pdbsum/2de4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de4 ProSAT]</span></td></tr> |
| - | <tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </span></td></tr>
| + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2de4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2de4 RCSB], [http://www.ebi.ac.uk/pdbsum/2de4 PDBsum]</span></td></tr> | + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/DSZB_RHOSG DSZB_RHOSG] Catalyzes the third and final step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Oxidizes 2-(2'-hydroxyphenyl)benzene sulphinate (HBPS) to 2-hydroxybiphenyl (HBP) plus sulfite (PubMed:31545606, PubMed:7574582, PubMed:7961424, PubMed:9308179, PubMed:9634856). The rate-limiting step of the '4S' desulfurization pathway (PubMed:31545606, PubMed:9308179). 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:31545606</ref> <ref>PMID:7574582</ref> <ref>PMID:7961424</ref> <ref>PMID:9308179</ref> <ref>PMID:9634856</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2de4_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/2de4_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> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2de4 ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 2de4" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Rhodococcus sp.]] | + | [[Category: Rhodococcus sp. IGTS8]] |
| - | [[Category: Izumi, Y.]] | + | [[Category: Izumi Y]] |
| - | [[Category: Lee, W C.]] | + | [[Category: Lee WC]] |
| - | [[Category: Matsubara, T.]] | + | [[Category: Matsubara T]] |
| - | [[Category: Ohshiro, T.]] | + | [[Category: Ohshiro T]] |
| - | [[Category: Tanokura, M.]] | + | [[Category: Tanokura M]] |
| - | [[Category: Alpha-beta]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
DSZB_RHOSG Catalyzes the third and final step of the '4S' desulfurization pathway that removes covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. Oxidizes 2-(2'-hydroxyphenyl)benzene sulphinate (HBPS) to 2-hydroxybiphenyl (HBP) plus sulfite (PubMed:31545606, PubMed:7574582, PubMed:7961424, PubMed:9308179, PubMed:9634856). The rate-limiting step of the '4S' desulfurization pathway (PubMed:31545606, PubMed:9308179). 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]
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
The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.
Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.,Lee WC, Ohshiro T, Matsubara T, Izumi Y, Tanokura M J Biol Chem. 2006 Oct 27;281(43):32534-9. Epub 2006 Aug 4. PMID:16891315[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
- ↑ Yu Y, Mills LC, Englert DL, Payne CM. Inhibition Mechanisms of Rhodococcus Erythropolis 2'-Hydroxybiphenyl-2-sulfinate Desulfinase (DszB). J Phys Chem B. 2019 Oct 31;123(43):9054-9065. PMID:31545606 doi:10.1021/acs.jpcb.9b05252
- ↑ 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
- ↑ 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
- ↑ Lee WC, Ohshiro T, Matsubara T, Izumi Y, Tanokura M. Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase. J Biol Chem. 2006 Oct 27;281(43):32534-9. Epub 2006 Aug 4. PMID:16891315 doi:10.1074/jbc.M602974200
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