5OEF

Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity.

Kertess, L.Wittkamp, F.Sommer, C.Esselborn, J.Rudiger, O.Reijerse, E.J.Hofmann, E.Lubitz, W.Winkler, M.Happe, T.Apfel, U.P.

(2017) Dalton Trans 46: 16947-16958

  • DOI: 10.1039/c7dt03785f

  • PubMed Abstract: 
  • [FeFe]-Hydrogenases efficiently catalyze the uptake and evolution of H <sub>2 </sub> due to the presence of an inorganic [6Fe-6S]-cofactor (H-cluster). This cofactor is comprised of a [4Fe-4S] cluster coupled to a unique [2Fe] cluster where the catal ...

    [FeFe]-Hydrogenases efficiently catalyze the uptake and evolution of H 2 due to the presence of an inorganic [6Fe-6S]-cofactor (H-cluster). This cofactor is comprised of a [4Fe-4S] cluster coupled to a unique [2Fe] cluster where the catalytic turnover of H 2 /H + takes place. We herein report on the synthesis of a selenium substituted [2Fe] cluster [Fe 2 {μ(SeCH 2 ) 2 NH}(CO) 4 (CN) 2 ] 2- (ADSe) and its successful in vitro integration into the native protein scaffold of [FeFe]-hydrogenases HydA1 from Chlamydomonas reinhardtii and CpI from Clostridium pasteurianum yielding fully active enzymes (HydA1-ADSe and CpI-ADSe). FT-IR spectroscopy and X-ray structure analysis confirmed the presence of structurally intact ADSe at the active site. Electrochemical assays reveal that the selenium containing enzymes are more biased towards hydrogen production than their native counterparts. In contrast to previous chalcogenide exchange studies, the S to Se exchange herein is not based on a simple reconstitution approach using ionic cluster constituents but on the in vitro maturation with a pre-synthesized selenium-containing [2Fe] mimic. The combination of biological and chemical methods allowed for the creation of a novel [FeFe]-hydrogenase with a [2Fe2Se]-active site which confers individual catalytic features.


    Organizational Affiliation

    Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany. Thomas.Happe@rub.de.,Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany.,Ruhr-Universität Bochum, Anorganische Chemie I/Bioanorganische Chemie, Universitätsstraße 150, 44801 Bochum, Germany. Ulf.Apfel@rub.de.,Ruhr-Universität Bochum, Lehrstuhl für Biophysik, AG Röntgenstrukturanalyse an Proteinen, Universitätsstraße 150, 44801 Bochum, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron hydrogenase 1
A, B
584Clostridium pasteurianumMutation(s): 0 
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
9SQ
Query on 9SQ

Download SDF File 
Download CCD File 
A, B
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 Se2
PHBGCQLNCRESHS-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
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 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 90.350α = 90.00
b = 72.880β = 98.70
c = 103.100γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC1069

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references
  • Version 1.2: 2017-12-20
    Type: Database references