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5ff4

From Proteopedia

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Current revision

HydE from T. maritima in complex with (2R,4R)-TMeTDA

Structural highlights

5ff4 is a 1 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.35Å
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

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/5ff4"

@@ Line 3: / Line 3: @@
 <StructureSection load='5ff4' size='340' side='right'caption='[[5ff4]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ff4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FF4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FF4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ff4]] 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=5FF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FF4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5ZZ:(2~{R},4~{R})-2,5,5-TRIMETHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC+ACID'>5ZZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene>, <scene name='pdbligand=SFS:FE4-SE4+CLUSTER'>SFS</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]] 1.35&#8491;</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]], [[5ff3|5ff3]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5ZZ:(2~{R},4~{R})-2,5,5-TRIMETHYL-1,3-THIAZOLIDINE-2,4-DICARBOXYLIC+ACID'>5ZZ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene>, <scene name='pdbligand=SFS:FE4-SE4+CLUSTER'>SFS</scene></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=2336 ATCC 43589])</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=5ff4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff4 OCA], [https://pdbe.org/5ff4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ff4 RCSB], [https://www.ebi.ac.uk/pdbsum/5ff4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff4 ProSAT]</span></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=5ff4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ff4 OCA], [http://pdbe.org/5ff4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ff4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ff4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ff4 ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
 [[Category: Large Structures]]
-[[Category: Amara, P]]
+[[Category: Thermotoga maritima]]
-[[Category: Benjdia, A]]
+[[Category: Amara P]]
-[[Category: Berteau, O]]
+[[Category: Benjdia A]]
-[[Category: Favier, A]]
+[[Category: Berteau O]]
-[[Category: Fontecilla-Camps, J C]]
+[[Category: Favier A]]
-[[Category: Martin, L]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Mouesca, J M]]
+[[Category: Martin L]]
-[[Category: Nicolet, Y]]
+[[Category: Mouesca JM]]
-[[Category: Rohac, R]]
+[[Category: Nicolet Y]]
-[[Category: Ruffie, P]]
+[[Category: Rohac R]]
-[[Category: Complex]]
+[[Category: Ruffie P]]
-[[Category: Fefe-hydrogenase maturase]]
-[[Category: Oxidoreductase]]
-[[Category: Radical sam enzyme]]
-[[Category: Thiazolidine]]

5ff4

From Proteopedia

Current revision

HydE from T. maritima in complex with (2R,4R)-TMeTDA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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