6GM6

[FeFe]-hydrogenase HydA1 from Chlamydomonas reinhardtii,variant E141Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases.

Duan, J.Senger, M.Esselborn, J.Engelbrecht, V.Wittkamp, F.Apfel, U.P.Hofmann, E.Stripp, S.T.Happe, T.Winkler, M.

(2018) Nat Commun 9: 4726-4726

  • DOI: https://doi.org/10.1038/s41467-018-07140-x
  • Primary Citation of Related Structures:  
    6GLY, 6GLZ, 6GM0, 6GM1, 6GM2, 6GM3, 6GM4, 6GM5, 6GM6, 6GM7, 6GM8

  • PubMed Abstract: 

    The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H 2 their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H 2 O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fe-hydrogenase452Chlamydomonas reinhardtiiMutation(s): 1 
Gene Names: hyd1HYD1hydAhydA1CHLRE_03g199800v5CHLREDRAFT_183963
EC: 1.18.99.1
UniProt
Find proteins for Q9FYU1 (Chlamydomonas reinhardtii)
Explore Q9FYU1 
Go to UniProtKB:  Q9FYU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FYU1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.79α = 90
b = 70.79β = 90
c = 155.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-15
    Changes: Advisory, Data collection, Database references, Derived calculations