This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5xdd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:18, 27 March 2024) (edit) (undo)
 
Line 1: Line 1:
==Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and Indole==
==Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and Indole==
-
<StructureSection load='5xdd' size='340' side='right' caption='[[5xdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+
<StructureSection load='5xdd' size='340' side='right'caption='[[5xdd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5xdd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Paenibacillus_sp._a11-2 Paenibacillus sp. a11-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XDD FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5xdd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_sp._A11-2 Paenibacillus sp. A11-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XDD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XDD 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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IND:INDOLE'>IND</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xdb|5xdb]], [[5xdc|5xdc]], [[5xde|5xde]], [[5xdg|5xdg]], [[5xb8|5xb8]]</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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IND:INDOLE'>IND</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tdsC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=107035 Paenibacillus sp. A11-2])</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=5xdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdd OCA], [https://pdbe.org/5xdd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xdd RCSB], [https://www.ebi.ac.uk/pdbsum/5xdd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdd 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=5xdd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdd OCA], [http://pdbe.org/5xdd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xdd RCSB], [http://www.ebi.ac.uk/pdbsum/5xdd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdd ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q9LBX2_9BACL Q9LBX2_9BACL]
-
Sulfur compounds in fossil fuels are a major source of environmental pollution, and microbial desulfurization has emerged as a promising technology for removing sulfur under mild conditions. The enzyme TdsC from the thermophile Paenibacillus sp. A11-2 is a two-component flavin-dependent monooxygenase that catalyzes the oxygenation of dibenzothiophene (DBT) to its sulfoxide (DBTO) and sulfone (DBTO2) during microbial desulfurization. The crystal structures of the apo and flavin mononucleotide (FMN)-bound forms of DszC, an ortholog of TdsC, were previously determined, although the structure of the ternary substrate-FMN-enzyme complex remains unknown. Herein, we report the crystal structures of the DBT-FMN-TdsC and DBTO-FMN-TdsC complexes. These ternary structures revealed many hydrophobic and hydrogen-bonding interactions with the substrate, and the position of the substrate could reasonably explain the two-step oxygenation of DBT by TdsC. We also determined the crystal structure of the indole-bound enzyme because TdsC, but not DszC, can also oxidize indole, and we observed that indole binding did not induce global conformational changes in TdsC with or without bound FMN. We also found that the two loop regions close to the FMN-binding site are disordered in apo-TdsC and become structured upon FMN binding. Alanine substitutions of Tyr-93 and His-388, which are located close to the substrate and FMN bound to TdsC, significantly decreased benzothiophene oxygenation activity, suggesting their involvement in supplying protons to the active site. Interestingly, these substitutions increased DBT oxygenation activity by TdsC, indicating that expanding the substrate-binding site can increase the oxygenation activity of TdsC on larger sulfur-containing substrates, a property that should prove useful for future microbial desulfurization applications.
+
-
 
+
-
Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity.,Hino T, Hamamoto H, Suzuki H, Yagi H, Ohshiro T, Nagano S J Biol Chem. 2017 Sep 22;292(38):15804-15813. doi: 10.1074/jbc.M117.788513. Epub , 2017 Aug 2. PMID:28768765<ref>PMID:28768765</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5xdd" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Paenibacillus sp. a11-2]]
+
[[Category: Large Structures]]
-
[[Category: Hamamoto, H]]
+
[[Category: Paenibacillus sp. A11-2]]
-
[[Category: Hino, T]]
+
[[Category: Hamamoto H]]
-
[[Category: Nagano, S]]
+
[[Category: Hino T]]
-
[[Category: Ohshiro, T]]
+
[[Category: Nagano S]]
-
[[Category: Fmn binding protein]]
+
[[Category: Ohshiro T]]
-
[[Category: Monooxygenase]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Tetramer]]
+

Current revision

Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and Indole

PDB ID 5xdd

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5xdd"
Personal tools