5FEP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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

    Metalloproteins Unit, Institut de Biologie Structurale, CEA, CNRS, UGA, 71 Avenue des Martyrs, 38044 Grenoble Cedex 9, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
[FeFe] hydrogenase maturase subunit HydE
A
358Thermotoga maritimaMutation(s): 3 
Gene Names: TM_1269THEMA_07990Tmari_1274
EC: 1.8
Find proteins for Q9X0Z6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X0Z6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download CCD File 
A
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
SAM
Query on SAM

Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
41K
Query on 41K

Download CCD File 
A
(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid
C6 H9 N O4 S
JCAKCGQZNBEITC-BBIVZNJYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.16α = 90
b = 80.02β = 90
c = 86.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BSV8-0013
French National Research AgencyFranceANR-10-INSB-05-02

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence