5MDJ

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in a its as-isolated high-pressurized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report



Literature

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase.

Kalms, J.Schmidt, A.Frielingsdorf, S.Utesch, T.Gotthard, G.von Stetten, D.van der Linden, P.Royant, A.Mroginski, M.A.Carpentier, P.Lenz, O.Scheerer, P.

(2018) Proc Natl Acad Sci U S A 115: E2229-E2237

  • DOI: 10.1073/pnas.1712267115
  • Primary Citation of Related Structures:  
    5MDK, 5MDJ, 5MDL

  • PubMed Abstract: 
  • [NiFe] hydrogenases catalyze the reversible splitting of H 2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogen ...

    [NiFe] hydrogenases catalyze the reversible splitting of H 2 into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O 2 , a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha , is able to overcome aerobic inactivation by catalytic reduction of O 2 to water. This O 2 tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O 2 attack. Here, the O 2 accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O 2 molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O 2 concentrations used for MBH crystal derivatization. The examination of the O 2 -derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O 2 tolerance of the enzyme.


    Organizational Affiliation

    Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, D-10117 Berlin, Germany; patrick.scheerer@charite.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uptake hydrogenase large subunit; HOXGL603Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxGPHG002
EC: 1.12.99.6
Find proteins for P31891 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / 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 subunit; HOXKS328Cupriavidus necator H16Mutation(s): 0 
Gene Names: hoxKPHG001
EC: 1.12.99.6
Find proteins for P31892 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / 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 CCD File 
S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F4S
Query on F4S

Download CCD File 
S
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFV
Query on NFV

Download CCD File 
L
NI-FE OXIDIZED ACTIVE CENTER
C3 Fe N2 Ni O2
MPQMGFDSXFFIQL-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.395α = 90
b = 95.696β = 90
c = 121.565γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCluster of Excellence - Unifying Concepts in Catalysis - UniCat - (EXC 314)
German Research FoundationGermanySFB 740 - B6

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 2.0: 2018-03-28
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.0: 2019-01-30
    Changes: Atomic model, Data collection, Derived calculations, Structure summary