5D51 | pdb_00005d51

Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network

• PDB DOI: https://doi.org/10.2210/pdb5D51/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cupriavidus necator
• Expression System: Cupriavidus necator
• Mutation(s): No 


• Deposited: 2015-08-10 Released: 2016-03-23 
• Deposition Author(s): Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., Scheerer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.

Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., Scheerer, P.

(2016) Angew Chem Int Ed Engl 55: 5586-5590

• PubMed: 26913499 
• DOI: https://doi.org/10.1002/anie.201508976
• Primary Citation Related Structures: 
  5D51


• PubMed Abstract: 
  

  [NiFe] hydrogenases are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and function of the tunnels is pivotal to modulating the feature of O2 tolerance in a subgroup of these [NiFe] hydrogenases, as they are interesting for developments in renewable energy technologies. Here we describe the crystal structure of the O2 -tolerant membrane-bound [NiFe] hydrogenase of Ralstonia eutropha (ReMBH), using krypton-pressurized crystals. The positions of the krypton atoms allow a comprehensive description of the tunnel network within the enzyme. A detailed overview of tunnel sizes, lengths, and routes is presented from tunnel calculations. A comparison of the ReMBH tunnel characteristics with crystal structures of other O2 -tolerant and O2 -sensitive [NiFe] hydrogenases revealed considerable differences in tunnel size and quantity between the two groups, which might be related to the striking feature of O2 tolerance.

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Organizational Affiliation: 
• Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany.
ESRF-European Synchrotron Radiation Facility, 71 Avenue des Martyrs, Grenoble Cedex 9, 38043, France.
Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.5 kDa 
• Atom Count: 7,534 
• Modeled Residue Count: 863 
• Deposited Residue Count: 942 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uptake hydrogenase large subunit	A [auth L]	603	Cupriavidus necator	Mutation(s): 0  Gene Names: hoxG, PHG002 EC: 1.12.99.6
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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uptake hydrogenase small subunit	B [auth S]	339	Cupriavidus necator	Mutation(s): 0  Gene Names: hoxK, PHG001 EC: 1.12.99.6
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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	R [auth S]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S	T [auth S]	FE4-S3 CLUSTER Fe4 S3 QQACTBFBZNWJMV-UHFFFAOYSA-N
F3S	S	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFV	C [auth L]	NI-FE OXIDIZED ACTIVE CENTER C3 Fe N2 Ni O2 MPQMGFDSXFFIQL-UHFFFAOYSA-N
KR	AA [auth S], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], O [auth L], P [auth L], U [auth S], V [auth S], W [auth S], X [auth S], Y [auth S], Z [auth S]	KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N
CL	BA [auth S], Q [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.387	α = 90
b = 95.574	β = 90
c = 119.752	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Kalms, J., Schmidt, A., Frielingsdorf, S., van der Linden, P., von Stetten, D., Lenz, O., Carpentier, P., Scheerer, P.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-03-30
  Changes: Database references
• Version 1.2: 2016-05-04
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description