4IUC

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase.

Frielingsdorf, S.Fritsch, J.Schmidt, A.Hammer, M.Lowenstein, J.Siebert, E.Pelmenschikov, V.Jaenicke, T.Kalms, J.Rippers, Y.Lendzian, F.Zebger, I.Teutloff, C.Kaupp, M.Bittl, R.Hildebrandt, P.Friedrich, B.Lenz, O.Scheerer, P.

(2014) Nat Chem Biol 10: 378-385

  • DOI: 10.1038/nchembio.1500
  • Primary Citation of Related Structures:  
    4IUB, 4IUC, 4IUD

  • PubMed Abstract: 
  • Hydrogenases catalyze the reversible oxidation of H(2) into protons and electrons and are usually readily inactivated by O(2). However, a subgroup of the [NiFe] hydrogenases, including the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha, has evolved remarkable tolerance toward O(2) that enables their host organisms to utilize H(2) as an energy source at high O(2) ...

    Hydrogenases catalyze the reversible oxidation of H(2) into protons and electrons and are usually readily inactivated by O(2). However, a subgroup of the [NiFe] hydrogenases, including the membrane-bound [NiFe] hydrogenase from Ralstonia eutropha, has evolved remarkable tolerance toward O(2) that enables their host organisms to utilize H(2) as an energy source at high O(2). This feature is crucially based on a unique six cysteine-coordinated [4Fe-3S] cluster located close to the catalytic center, whose properties were investigated in this study using a multidisciplinary approach. The [4Fe-3S] cluster undergoes redox-dependent reversible transformations, namely iron swapping between a sulfide and a peptide amide N. Moreover, our investigations unraveled the redox-dependent and reversible occurence of an oxygen ligand located at a different iron. This ligand is hydrogen bonded to a conserved histidine that is essential for H(2) oxidation at high O(2). We propose that these transformations, reminiscent of those of the P-cluster of nitrogenase, enable the consecutive transfer of two electrons within a physiological potential range.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik (CharitéCrossOver), AG Proteinstrukturanalyse, Charité-Universitätsmedizin Berlin, Berlin, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uptake hydrogenase large subunitA [auth L]603Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxGPHG002
EC: 1.12.5.1 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for P31891 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore P31891 
Go to UniProtKB:  P31891
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uptake hydrogenase small subunitB [auth S]339Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxKPHG001
EC: 1.12.5.1 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for P31892 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore P31892 
Go to UniProtKB:  P31892
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
F [auth S]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
S3F (Subject of Investigation/LOI)
Query on S3F

Download Ideal Coordinates CCD File 
H [auth S]oxidized [Fe4-S3] cluster
Fe4 O S3
ROWMPBKAWWBNCP-UHFFFAOYSA-M
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
G [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFV (Subject of Investigation/LOI)
Query on NFV

Download Ideal Coordinates CCD File 
C [auth L]NI-FE OXIDIZED ACTIVE CENTER
C3 Fe N2 Ni O2
MPQMGFDSXFFIQL-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth L], I [auth S]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.618α = 90
b = 95.742β = 90
c = 120.702γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description