5FF0 | pdb_00005ff0

HydE from T. maritima in complex with S-adenosyl-L-cysteine and methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 
    0.169 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.150 (Depositor) 
  • R-Value Observed: 
    0.151 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 45.21 kDa 
  • Atom Count: 3,703 
  • Modeled Residue Count: 346 
  • Deposited Residue Count: 358 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 5 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],
K [auth A]
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
SFS

Query on SFS



Download:Ideal Coordinates CCD File
B [auth A]Fe4-Se4 cluster
Fe4 Se4
HSQOKLBIIKAQNG-UHFFFAOYSA-N
5X8

Query on 5X8



Download:Ideal Coordinates CCD File
J [auth A]S-adenosyl-L-cysteine
C13 H18 N6 O5 S
RVFHZLGRQFCOKV-MACXSXHHSA-N
MET

Query on MET



Download:Ideal Coordinates CCD File
I [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free:  0.169 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.150 (Depositor) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.89α = 90
b = 79.34β = 90
c = 86.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: Advisory, Data collection, Database references, Refinement description