4XDC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.

Esselborn, J.Muraki, N.Klein, K.Engelbrecht, V.Metzler-Nolte, N.Apfel, U.P.Hofmann, E.Kurisu, G.Happe, T.

(2016) Chem Sci 7: 959-968

  • DOI: 10.1039/c5sc03397g
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • [FeFe]-hydrogenases are nature's fastest catalysts for the evolution or oxidation of hydrogen. Numerous synthetic model complexes for the [2Fe] subcluster (2Fe <sub>H </sub>) of their active site are known, but so far none of these could compete with ...

    [FeFe]-hydrogenases are nature's fastest catalysts for the evolution or oxidation of hydrogen. Numerous synthetic model complexes for the [2Fe] subcluster (2Fe H ) of their active site are known, but so far none of these could compete with the enzymes. The complex Fe 2 [μ-(SCH 2 ) 2 X](CN) 2 (CO) 4 2- with X = NH was shown to integrate into the apo-form of [FeFe]-hydrogenases to yield a fully active enzyme. Here we report the first crystal structures of the apo-form of the bacterial [FeFe]-hydrogenase CpI from Clostridium pasteurianum at 1.60 Å and the active semisynthetic enzyme, CpI ADT , at 1.63 Å. The structures illustrate the significant changes in ligand coordination upon integration and activation of the [2Fe] complex. These changes are induced by a rigid 2Fe H cavity as revealed by the structure of apoCpI, which is remarkably similar to CpI ADT . Additionally we present the high resolution crystal structures of the semisynthetic bacterial [FeFe]-hydrogenases CpI PDT (X = CH 2 ), CpI ODT (X = O) and CpI SDT (X = S) with changes in the headgroup of the dithiolate bridge in the 2Fe H cofactor. The structures of these inactive enzymes demonstrate that the 2Fe H -subcluster and its protein environment remain largely unchanged when compared to the active enzyme CpI ADT . As the active site shows an open coordination site in all structures, the absence of catalytic activity is probably not caused by steric obstruction. This demonstrates that the chemical properties of the dithiolate bridge are essential for enzyme activity.


    Organizational Affiliation

    Laboratory of Protein Crystallography , Institute for Protein Research , Osaka University , Suita , Osaka 565-0871 , Japan . Email: gkurisu@protein.Osaka-u.ac.,Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie , Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . Email: ulf.apfel@rub.de.,AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . Email: thomas.happe@rub.de.,AG Proteinkristallographie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , 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

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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

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

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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: 1.63 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 91.340α = 90.00
b = 73.650β = 97.28
c = 103.880γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references