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6q1l

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Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and 3-iodo-L-tyrosine

Structural highlights

6q1l is a 2 chain structure with sequence from Thermotoga neapolitana DSM 4359. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1]

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sun Z, Xu B, Spisak S, Kavran JM, Rokita SE. The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana. J Biol Chem. 2021 Dec;297(6):101385. doi: 10.1016/j.jbc.2021.101385. Epub 2021, Nov 6. PMID:34748729 doi:http://dx.doi.org/10.1016/j.jbc.2021.101385
↑ Sun Z, Xu B, Spisak S, Kavran JM, Rokita SE. The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana. J Biol Chem. 2021 Dec;297(6):101385. doi: 10.1016/j.jbc.2021.101385. Epub 2021, Nov 6. PMID:34748729 doi:http://dx.doi.org/10.1016/j.jbc.2021.101385

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6q1l"

Categories: Large Structures | Thermotoga neapolitana DSM 4359 | Kavran JM | Rokita SE | Sun Z

@@ Line 3: / Line 3: @@
 <StructureSection load='6q1l' size='340' side='right'caption='[[6q1l]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6q1l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thenn Thenn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q1L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6q1l]] 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=6Q1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q1L FirstGlance]. <br>
-</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=IYR:3-IODO-TYROSINE'>IYR</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]] 1.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CTN_0569 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=309803 THENN])</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=IYR:3-IODO-TYROSINE'>IYR</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=6q1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q1l OCA], [https://pdbe.org/6q1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q1l RCSB], [https://www.ebi.ac.uk/pdbsum/6q1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q1l ProSAT]</span></td></tr>
 </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 ==
@@ Line 22: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thenn]]
+[[Category: Thermotoga neapolitana DSM 4359]]
-[[Category: Kavran, J M]]
+[[Category: Kavran JM]]
-[[Category: Rokita, S E]]
+[[Category: Rokita SE]]
-[[Category: Sun, Z]]
+[[Category: Sun Z]]
-[[Category: Dehalogenase]]
-[[Category: Flavoprotein]]
-[[Category: Halotyrosine]]
-[[Category: Oxidoreductase]]
-[[Category: Thermophile]]

6q1l

From Proteopedia

Current revision

Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and 3-iodo-L-tyrosine

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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