6pz0
From Proteopedia
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==Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and L-Tyrosine== | ==Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and L-Tyrosine== | ||
| - | <StructureSection load='6pz0' size='340' side='right'caption='[[6pz0]]' scene=''> | + | <StructureSection load='6pz0' size='340' side='right'caption='[[6pz0]], [[Resolution|resolution]] 1.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PZ0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pz0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_neapolitana_DSM_4359 Thermotoga neapolitana DSM 4359]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PZ0 FirstGlance]. <br> |
| - | </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=6pz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pz0 OCA], [https://pdbe.org/6pz0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pz0 RCSB], [https://www.ebi.ac.uk/pdbsum/6pz0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pz0 ProSAT]</span></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]] 1.8Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene></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=6pz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pz0 OCA], [https://pdbe.org/6pz0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pz0 RCSB], [https://www.ebi.ac.uk/pdbsum/6pz0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pz0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/IYD_THENN IYD_THENN] Catalyzes the dehalogenation of halotyrosines such as 3-bromo-L-tyrosine, 3-chloro-L-tyrosine, 3-iodo-L-tyrosine and 3,5-diiodo-L-tyrosine (PubMed:34748729). Activity towards 2-iodophenol is weak (PubMed:34748729).<ref>PMID:34748729</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The nitroreductase superfamily of enzymes encompasses many flavin mononucleotide (FMN)-dependent catalysts promoting a wide range of reactions. All share a common core consisting of an FMN-binding domain, and individual subgroups additionally contain one to three sequence extensions radiating from defined positions within this core to support their unique catalytic properties. To identify the minimum structure required for activity in the iodotyrosine deiodinase subgroup of this superfamily, attention was directed to a representative from the thermophilic organism Thermotoga neapolitana (TnIYD). This representative was selected based on its status as an outlier of the subgroup arising from its deficiency in certain standard motifs evident in all homologues from mesophiles. We found that TnIYD lacked a typical N-terminal sequence and one of its two characteristic sequence extensions, neither of which was found to be necessary for activity. We also show that TnIYD efficiently promotes dehalogenation of iodo-, bromo-, and chlorotyrosine, analogous to related deiodinases (IYDs) from humans and other mesophiles. In addition, 2-iodophenol is a weak substrate for TnIYD as it was for all other IYDs characterized to date. Consistent with enzymes from thermophilic organisms, we observed that TnIYD adopts a compact fold and low surface area compared with IYDs from mesophilic organisms. The insights gained from our investigations on TnIYD demonstrate the advantages of focusing on sequences that diverge from conventional standards to uncover the minimum essentials for activity. We conclude that TnIYD now represents a superior starting structure for future efforts to engineer a stable dehalogenase targeting halophenols of environmental concern. | ||
| + | |||
| + | The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana.,Sun Z, Xu B, Spisak S, Kavran JM, Rokita SE J Biol Chem. 2021 Dec;297(6):101385. doi: 10.1016/j.jbc.2021.101385. Epub 2021, Nov 6. PMID:34748729<ref>PMID:34748729</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6pz0" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Thermotoga neapolitana DSM 4359]] | ||
[[Category: Kavran JM]] | [[Category: Kavran JM]] | ||
[[Category: Rokita SE]] | [[Category: Rokita SE]] | ||
[[Category: Sun Z]] | [[Category: Sun Z]] | ||
Current revision
Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and L-Tyrosine
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