2de2: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='2de2' size='340' side='right'caption='[[2de2]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2de2' size='340' side='right'caption='[[2de2]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2de2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhosg Rhosg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2de2]] is a 1 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=2DE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DE2 FirstGlance]. <br>
</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=GOL:GLYCEROL'>GOL</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]] 1.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2de3|2de3]], [[2de4|2de4]]</div></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=GOL:GLYCEROL'>GOL</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DSZB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54064 RHOSG])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/2'-hydroxybiphenyl-2-sulfinate_desulfinase 2'-hydroxybiphenyl-2-sulfinate desulfinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.13.1.3 3.13.1.3] </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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [https://pdbe.org/2de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [https://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 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=2de2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2de2 OCA], [https://pdbe.org/2de2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2de2 RCSB], [https://www.ebi.ac.uk/pdbsum/2de2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2de2 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/SOXB_RHOSG SOXB_RHOSG]] Part of a pathway to remove covalently bound sulfur from dibenzothiophene (DBT) without breaking carbon-carbon bonds. This enzyme metabolizes DBT-sulfone (DBTO2 or DBT 5,5-dioxide) to 2-hydroxybiphenyl (2-HBP).  
[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:7961424, PubMed:7574582, PubMed:9634856, PubMed:9308179, PubMed:31545606). The rate-limiting step of the '4S' desulfurization pathway (PubMed:9308179, PubMed:31545606). 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]]
Line 22: Line 20:
</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=2de2 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=2de2 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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<ref>PMID:16891315</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2de2" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 2'-hydroxybiphenyl-2-sulfinate desulfinase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rhosg]]
[[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]]
Retrieved from "https://proteopedia.org/2de2"