5KH0 | pdb_00005kh0

Crystal Structure of HydF from thermosipho melanesiensis in complex with a [4Fe-4S] cluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.262 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5KH0

This is version 1.4 of the entry. See complete history

Literature

Structural and functional characterization of the hydrogenase-maturation HydF protein.

Caserta, G.Pecqueur, L.Adamska-Venkatesh, A.Papini, C.Roy, S.Artero, V.Atta, M.Reijerse, E.Lubitz, W.Fontecave, M.

(2017) Nat Chem Biol 13: 779-784

  • DOI: https://doi.org/10.1038/nchembio.2385
  • Primary Citation Related Structures: 
    5KH0, 5LAD

  • PubMed Abstract: 

    [FeFe] hydrogenase (HydA) catalyzes interconversion between 2H + and H 2 at an active site composed of a [4Fe-4S] cluster linked to a 2Fe subcluster that harbors CO, CN - and azapropanedithiolate (adt 2- ) ligands. HydE, HydG and HydF are the maturases specifically involved in the biosynthesis of the 2Fe subcluster. Using ligands synthesized by HydE and HydG, HydF assembles a di-iron precursor of the 2Fe subcluster and transfers it to HydA for maturation. Here we report the first X-ray structure of HydF with its [4Fe-4S] cluster. The cluster is chelated by three cysteines and an exchangeable glutamate, which allows the binding of synthetic mimics of the 2Fe subcluster. [Fe 2 (adt)(CO) 4 (CN) 2 ] 2- is proposed to be the true di-iron precursor because, when bound to HydF, it matures HydA and displays features in Fourier transform infrared (FTIR) spectra that are similar to those of the native HydF active intermediate. A new route toward the generation of artificial hydrogenases, as combinations of HydF and such biomimetic complexes, is proposed on the basis of the observed hydrogenase activity of chemically modified HydF.


  • Organizational Affiliation
    • Laboratoire de Chimie des Processus Biologiques, Collège de France, Université Pierre et Marie Curie, CNRS UMR 8229, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 178.83 kDa 
  • Atom Count: 11,371 
  • Modeled Residue Count: 1,438 
  • Deposited Residue Count: 1,584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Small GTP-binding protein
A, B, C, D
396Thermosipho melanesiensis BI429Mutation(s): 0 
Gene Names: Tmel_1361
UniProt
Find proteins for A6LMQ7 (Thermosipho melanesiensis (strain DSM 12029 / CIP 104789 / BI429))
Explore A6LMQ7 
Go to UniProtKB:  A6LMQ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6LMQ7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.262 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.01α = 90
b = 173.48β = 110.01
c = 89.32γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references
  • Version 1.3: 2017-06-28
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references