6TTL

crystal structure of [FeFe]-hydrogenase CbA5H (partial) from Clostridium beijerinckii in Hinact state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.339 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A safety cap protects hydrogenase from oxygen attack.

Winkler, M.Duan, J.Rutz, A.Felbek, C.Scholtysek, L.Lampret, O.Jaenecke, J.Apfel, U.P.Gilardi, G.Valetti, F.Fourmond, V.Hofmann, E.Leger, C.Happe, T.

(2021) Nat Commun 12: 756-756

  • DOI: https://doi.org/10.1038/s41467-020-20861-2
  • Primary Citation of Related Structures:  
    6TTL

  • PubMed Abstract: 

    [FeFe]-hydrogenases are efficient H 2 -catalysts, yet upon contact with dioxygen their catalytic cofactor (H-cluster) is irreversibly inactivated. Here, we combine X-ray crystallography, rational protein design, direct electrochemistry, and Fourier-transform infrared spectroscopy to describe a protein morphing mechanism that controls the reversible transition between the catalytic H ox -state and the inactive but oxygen-resistant H inact -state in [FeFe]-hydrogenase CbA5H of Clostridium beijerinckii. The X-ray structure of air-exposed CbA5H reveals that a conserved cysteine residue in the local environment of the active site (H-cluster) directly coordinates the substrate-binding site, providing a safety cap that prevents O 2 -binding and consequently, cofactor degradation. This protection mechanism depends on three non-conserved amino acids situated approximately 13 Å away from the H-cluster, demonstrating that the 1st coordination sphere chemistry of the H-cluster can be remote-controlled by distant residues.


  • Organizational Affiliation

    Photobiotechnology, Department of Plant Biochemistry, Ruhr-Universität Bochum, 44801, Bochum, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[FeFe]-hydrogenase
A, B
674Clostridium beijerinckiiMutation(s): 0 
UniProt
Find proteins for A0A1I9RYV3 (Clostridium beijerinckii)
Explore A0A1I9RYV3 
Go to UniProtKB:  A0A1I9RYV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I9RYV3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.339 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169α = 90
b = 169β = 90
c = 127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2021-02-17
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description