5FEZ

HydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyadenosine and methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPSClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view detailsBest fitted 9SEClick on this verticalbar to view details

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: https://doi.org/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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[FeFe] hydrogenase maturase subunit HydE358Thermotoga maritimaMutation(s): 3 
Gene Names: TM_1269THEMA_07990Tmari_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0Z6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS
Query on CPS

Download Ideal Coordinates CCD File 
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
SFS
Query on SFS

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B [auth A]Fe4-Se4 cluster
Fe4 Se4
HSQOKLBIIKAQNG-UHFFFAOYSA-N
5AD
Query on 5AD

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I [auth A]5'-DEOXYADENOSINE
C10 H13 N5 O3
XGYIMTFOTBMPFP-KQYNXXCUSA-N
9SE
Query on 9SE

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K [auth A](2~{R},4~{R})-2-methyl-1,3-selenazolidine-2,4-dicarboxylic acid
C6 H9 N O4 Se
YQSKWMPEENRPTH-BBIVZNJYSA-N
MET
Query on MET

Download Ideal Coordinates CCD File 
J [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
CL
Query on CL

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H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.135 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.8α = 90
b = 78.87β = 90
c = 86.25γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPSClick on this verticalbar to view detailsBest fitted 5ADClick on this verticalbar to view detailsBest fitted 9SEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description