4IUB

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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). 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

    1] Institut für Biologie-Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany. [2] Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31891
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31892
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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J [auth S]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
S3F
Query on S3F

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L [auth S]oxidized [Fe4-S3] cluster
Fe4 O S3
ROWMPBKAWWBNCP-UHFFFAOYSA-M
F3S
Query on F3S

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K [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFV
Query on NFV

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C [auth L]NI-FE OXIDIZED ACTIVE CENTER
C3 Fe N2 Ni O2
MPQMGFDSXFFIQL-UHFFFAOYSA-N
PO4
Query on PO4

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E [auth L]
F [auth L]
G [auth L]
H [auth L]
I [auth L]
E [auth L],
F [auth L],
G [auth L],
H [auth L],
I [auth L],
M [auth S]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

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N [auth S]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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D [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.903α = 90
b = 95.39β = 90
c = 118.818γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description