5BYR | pdb_00005byr

Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor

• PDB DOI: https://doi.org/10.2210/pdb5BYR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium pasteurianum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-10 Released: 2015-11-11 
• Deposition Author(s): Esselborn, J., Muraki, N., Engelbrecht, V., Hofmann, E., Kurisu, G., Happe, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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

• PubMed: 29896366 
• DOI: https://doi.org/10.1039/c5sc03397g
• Primary Citation Related Structures: 
  4XDC, 4XDD, 5BYQ, 5BYR, 5BYS


• 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 _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.

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Organizational Affiliation: 
• AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . Email: [e-mail].
Laboratory of Protein Crystallography , Institute for Protein Research , Osaka University , Suita , Osaka 565-0871 , Japan . Email: [e-mail].
Lehrstuhl für Anorganische Chemie I-Bioanorganische Chemie , Fakultät für Chemie und Biochemie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . Email: [e-mail].
AG Proteinkristallographie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 134.4 kDa 
• Atom Count: 9,859 
• Modeled Residue Count: 1,143 
• Deposited Residue Count: 1,168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron hydrogenase 1	A, B	584	Clostridium pasteurianum	Mutation(s): 0  EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum) Explore P29166  Go to UniProtKB:  P29166

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WW	H [auth A], S [auth B]	bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+) C8 H6 Fe2 N2 O3 S2 POEKPSQXPZCVMK-UHFFFAOYSA-N
SF4	C [auth A], D [auth A], E [auth A], F [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	G [auth A], R [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	I [auth A], J [auth A], K [auth A], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.47	α = 90
b = 72.07	β = 100.86
c = 102.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Esselborn, J., Muraki, N., Engelbrecht, V., Hofmann, E., Kurisu, G., Happe, T.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection
• Version 1.2: 2018-07-11
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary