5FF3

HydE from T. maritima in complex with 4R-TCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

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, J.M.Fontecilla-Camps, J.C.Nicolet, Y.

(2016) Nat.Chem. 8: 491-500

  • DOI: 10.1038/nchem.2490
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Biomolecular NMR Spectroscopy Group, Institut de Biologie Structurale, CEA, CNRS, UGA, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, F-78350 Jouy-en-Josas, France.,CEA, INAC, SCIB/LRM, F-38054 Grenoble, France.,Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, UGA, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France.,Université Grenoble Alpes, INAC, SCIB/LRM, F-38000 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
[FeFe] hydrogenase maturase subunit HydE
A
348Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
EC: 1.8.-.-
Find proteins for Q9X0Z6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X0Z6
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
H2S
Query on H2S

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Download CCD File 
A
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PRS
Query on PRS

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A
THIOPROLINE
C4 H7 N O2 S
DZLNHFMRPBPULJ-VKHMYHEASA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
CPS
Query on CPS

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A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OTY
Query on OTY
A
L-PEPTIDE LINKINGC9 H11 N O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.000α = 90.00
b = 79.190β = 90.00
c = 86.240γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-04
    Type: Database references
  • Version 2.0: 2019-02-06
    Type: Atomic model, Data collection, Derived calculations