Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.08 kDa 
• Atom Count: 3726 
• Modelled Residue Count: 346 
• Deposited Residue Count: 358 
• Unique protein chains: 1

5FEP

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

• PDB DOI: 10.2210/pdb5FEP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-12-17 Released: 2016-04-06 
• Deposition Author(s): Rohac, R., Amara, P., Benjdia, A., Martin, L., Ruffie, P., Favier, A., Berteau, O., Mouesca, J.M., Fontecilla-Camps, J.C., Nicolet, Y.
• Funding Organization(s): French National Research Agency

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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 

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

• PubMed: 27102684 
• DOI: 10.1038/nchem.2490
• Primary Citation of Related Structures:  
  5FEP, 5FES, 5FEW, 5FEX, 5FEZ, 5FF0, 5FF2, 5FF3, 5FF4


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[FeFe] hydrogenase maturase subunit HydE	A	358	Thermotoga maritima	Mutation(s): 3  Gene Names: TM_1269, THEMA_07990, Tmari_1274 EC: 1.8
UniProt
Find proteins for Q9X0Z6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0Z6  Go to UniProtKB:  Q9X0Z6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
SAM	H [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
41K	J [auth A]	(2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid C6 H9 N O4 S JCAKCGQZNBEITC-BBIVZNJYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 51.16	α = 90
b = 80.02	β = 90
c = 86.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-12-17 
• Released Date: 2016-04-06 
Deposition Author(s): Rohac, R., Amara, P., Benjdia, A., Martin, L., Ruffie, P., Favier, A., Berteau, O., Mouesca, J.M., Fontecilla-Camps, J.C., Nicolet, Y.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-12-BSV8-0013
French National Research Agency	France	ANR-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