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| | <StructureSection load='5ff3' size='340' side='right'caption='[[5ff3]], [[Resolution|resolution]] 1.18Å' scene=''> | | <StructureSection load='5ff3' size='340' side='right'caption='[[5ff3]], [[Resolution|resolution]] 1.18Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ff3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FF3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ff3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FF3 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=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=PRS:THIOPROLINE'>PRS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.18Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=OTY:2-HYDROXY-L-TYROSINE'>OTY</scene></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=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=OTY:2-HYDROXY-L-TYROSINE'>OTY</scene>, <scene name='pdbligand=PRS:THIOPROLINE'>PRS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3iix|3iix]], [[3iiz|3iiz]], [[5fep|5fep]], [[5fes|5fes]], [[5few|5few]], [[5fex|5fex]], [[5fez|5fez]], [[5ff0|5ff0]], [[5ff2|5ff2]]</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=5ff3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff3 OCA], [https://pdbe.org/5ff3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ff3 RCSB], [https://www.ebi.ac.uk/pdbsum/5ff3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff3 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TM_1269, THEMA_07990, Tmari_1274 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ff3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff3 OCA], [http://pdbe.org/5ff3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ff3 RCSB], [http://www.ebi.ac.uk/pdbsum/5ff3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff3 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 26: |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thema]] | + | [[Category: Thermotoga maritima MSB8]] |
| - | [[Category: Amara, P]] | + | [[Category: Amara P]] |
| - | [[Category: Benjdia, A]] | + | [[Category: Benjdia A]] |
| - | [[Category: Berteau, O]] | + | [[Category: Berteau O]] |
| - | [[Category: Favier, A]] | + | [[Category: Favier A]] |
| - | [[Category: Fontecilla-Camps, J C]] | + | [[Category: Fontecilla-Camps JC]] |
| - | [[Category: Martin, L]] | + | [[Category: Martin L]] |
| - | [[Category: Mouesca, J M]] | + | [[Category: Mouesca JM]] |
| - | [[Category: Nicolet, Y]] | + | [[Category: Nicolet Y]] |
| - | [[Category: Rohac, R]] | + | [[Category: Rohac R]] |
| - | [[Category: Ruffie, P]] | + | [[Category: Ruffie P]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Fefe-hydrogenase maturase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Radical sam enzyme]]
| + | |
| - | [[Category: Thiazolidine]]
| + | |
| Structural highlights
5ff3 is a 1 chain structure with sequence from Thermotoga maritima MSB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.18Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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][1]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Rubach JK, Brazzolotto X, Gaillard J, Fontecave M. Biochemical characterization of the HydE and HydG iron-only hydrogenase maturation enzymes from Thermatoga maritima. FEBS Lett. 2005 Sep 12;579(22):5055-60. PMID:16137685 doi:http://dx.doi.org/10.1016/j.febslet.2005.07.092
- ↑ Rohac R, Amara P, Benjdia A, Martin L, Ruffie P, Favier A, Berteau O, Mouesca JM, Fontecilla-Camps JC, Nicolet Y. Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE. Nat Chem. 2016 May;8(5):491-500. doi: 10.1038/nchem.2490. Epub 2016 Apr 4. PMID:27102684 doi:http://dx.doi.org/10.1038/nchem.2490
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