5fep: Difference between revisions
New page: '''Unreleased structure''' The entry 5fep is ON HOLD Authors: Rohac, R., Amara, P., Benjdia, A., Martin, L., Ruffie, P., Favier, A., Berteau, O., Mouesca, J.M., Fontecilla-Camps, J.C., ... |
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==HydE from T. maritima in complex with (2R,4R)-MeTDA== | |||
<StructureSection load='5fep' size='340' side='right'caption='[[5fep]], [[Resolution|resolution]] 1.45Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5fep]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FEP FirstGlance]. <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]] 1.45Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=41K:(2R,4R)-2-METHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC+ACID'>41K</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=OTY:2-HYDROXY-L-TYROSINE'>OTY</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5fep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fep OCA], [https://pdbe.org/5fep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fep RCSB], [https://www.ebi.ac.uk/pdbsum/5fep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fep ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/HYDE_THEMA HYDE_THEMA] Required for the maturation of the [FeFe]-hydrogenase HydA (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-methionine (in vitro), suggesting it may contribute to the biosynthesis of an essential sulfur-containing ligand that binds to the hydrogenase active site [2Fe-2S] cluster (PubMed:16137685).[UniProtKB:Q97IK9]<ref>PMID:16137685</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate. | |||
Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.,Rohac R, Amara P, Benjdia A, Martin L, Ruffie P, Favier A, Berteau O, Mouesca JM, Fontecilla-Camps JC, Nicolet Y Nat Chem. 2016 May;8(5):491-500. doi: 10.1038/nchem.2490. Epub 2016 Apr 4. PMID:27102684<ref>PMID:27102684</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5fep" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: Berteau | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermotoga maritima]] | ||
[[Category: | [[Category: Amara P]] | ||
[[Category: | [[Category: Benjdia A]] | ||
[[Category: | [[Category: Berteau O]] | ||
[[Category: Favier A]] | |||
[[Category: Fontecilla-Camps JC]] | |||
[[Category: Martin L]] | |||
[[Category: Mouesca JM]] | |||
[[Category: Nicolet Y]] | |||
[[Category: Rohac R]] | |||
[[Category: Ruffie P]] | |||
Latest revision as of 09:48, 19 July 2023
HydE from T. maritima in complex with (2R,4R)-MeTDAHydE from T. maritima in complex with (2R,4R)-MeTDA
Structural highlights
FunctionHYDE_THEMA Required for the maturation of the [FeFe]-hydrogenase HydA (By similarity). Catalyzes the reductive cleavage of S-adenosyl-L-methionine (in vitro), suggesting it may contribute to the biosynthesis of an essential sulfur-containing ligand that binds to the hydrogenase active site [2Fe-2S] cluster (PubMed:16137685).[UniProtKB:Q97IK9][1] Publication Abstract from PubMedCarbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate. Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.,Rohac R, Amara P, Benjdia A, Martin L, Ruffie P, Favier A, Berteau O, Mouesca JM, Fontecilla-Camps JC, Nicolet Y Nat Chem. 2016 May;8(5):491-500. doi: 10.1038/nchem.2490. Epub 2016 Apr 4. PMID:27102684[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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