6GM2

[FeFe]-hydrogenase CpI from Clostridium pasteurianum, variant E282D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-018-07140-x
  • Primary Citation of Related Structures:  

  • 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 ...

    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. thomas.happe@rub.de.,Department of Biophysics, Protein Crystallography, Ruhr-Universität Bochum, 44801, Bochum, Germany.,Fraunhofer UMSICHT, Osterfelder Straße, 346047, Oberhausen, Germany.,Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195, Berlin, Germany.,Department of Chemistry and Biochemistry, Inorganic Chemistry Ι, Ruhr-Universität Bochum, 44801, Bochum, Germany.,Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany.,Department of Plant Biochemistry, Photobiotechnology, Ruhr-Universität Bochum, 44801, Bochum, Germany. martin.winkler-2@rub.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron hydrogenase 1
A, B
584Clostridium pasteurianumMutation(s): 1 
EC: 1.12.7.2
Find proteins for P29166 (Clostridium pasteurianum)
Go to UniProtKB:  P29166
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A, B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
402
Query on 402

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Download CCD File 
A, B
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 S2
LJPDYWPSPOWMIB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.870α = 90.00
b = 72.820β = 96.86
c = 102.910γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references