4UQL | pdb_00004uql

High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant

• PDB DOI: https://doi.org/10.2210/pdb4UQL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Solidesulfovibrio fructosivorans
• Expression System: Solidesulfovibrio fructosivorans
• Mutation(s): Yes 


• Deposited: 2014-06-24 Released: 2014-10-29 
• Deposition Author(s): Volbeda, A., Martin, L., Barbier, E., Gutierrez-Sanz, O., DeLacey, A.L., Liebgott, P.P., Dementin, S., Rousset, M., Fontecilla-Camps, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.152 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures for the Elusive Unready Oxidized States.

Volbeda, A., Martin, L., Barbier, E., Gutierrez-Sanz, O., De Lacey, A.L., Liebgott, P., Dementin, S., Rousset, M., Fontecilla-Camps, J.C.

(2015) J Biol Inorg Chem 20: 11

• PubMed: 25315838 
• DOI: https://doi.org/10.1007/s00775-014-1203-9
• Primary Citation Related Structures: 
  4UPE, 4UPV, 4UQL, 4UQP, 4URH


• PubMed Abstract: 
  

  Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.

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Organizational Affiliation: 
• University Grenoble Alpes, IBS, 38044, Grenoble, France. [e-mail].
CEA, IBS, 38044, Grenoble, France. [e-mail].
CNRS, IBS, 38044, Grenoble, France. [e-mail].
University Grenoble Alpes, IBS, 38044, Grenoble, France.
CEA, IBS, 38044, Grenoble, France.
CNRS, IBS, 38044, Grenoble, France.
CEA, MINATEC, 38044, Grenoble, France.
Instituto de Catálisis y Petroleoquímica, CSIC, 28049, Madrid, Spain.
Aix-Marseille Université, CNRS, IMM, 13402, Marseille, France.
Aix-Marseille Université, CNRS/INSU, MIO, 13288, Marseille, France.
Consulate General of France, 205 N Michigan Ave, Chicago, IL, 60601, USA.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 183.13 kDa 
• Atom Count: 14,688 
• Modeled Residue Count: 1,614 
• Deposited Residue Count: 1,656 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE (NIFE) SMALL SUBUNIT HYDA	A, B	265	Solidesulfovibrio fructosivorans	Mutation(s): 0  EC: 1.12.2.1
UniProt
Find proteins for P18187 (Solidesulfovibrio fructosivorans) Explore P18187  Go to UniProtKB:  P18187

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT	C [auth Q], D [auth R]	563	Solidesulfovibrio fructosivorans	Mutation(s): 1  EC: 1.12.2.1
UniProt
Find proteins for P18188 (Solidesulfovibrio fructosivorans) Explore P18188  Go to UniProtKB:  P18188

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	E [auth A], G [auth A], K [auth B], M [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	F [auth A], L [auth B]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
SOT	N [auth B]	morpholine-4-sulfonic acid C4 H9 N O4 S GLGNSAPAWZUDRT-UHFFFAOYSA-N
FCO	T [auth Q], Z [auth R]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
GOL	CA [auth R], DA [auth R], EA [auth R], FA [auth R], GA [auth R], H [auth A], I [auth A], O [auth B], P [auth B], R [auth B], W [auth Q]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY	J [auth B], S [auth Q], Y [auth R]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
NI	AA [auth R], U [auth Q]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	X [auth Q]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S	Q [auth B]	HYDROSULFURIC ACID H2 S RWSOTUBLDIXVET-UHFFFAOYSA-N
MG	BA [auth R], V [auth Q]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	C [auth Q], D [auth R]	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS
CSX	C [auth Q], D [auth R]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.152 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.69	α = 90
b = 100.85	β = 105.96
c = 116.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Volbeda, A., Martin, L., Barbier, E., Gutierrez-Sanz, O., DeLacey, A.L., Liebgott, P.P., Dementin, S., Rousset, M., Fontecilla-Camps, J.C.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2015-01-21
  Changes: Database references
• Version 1.2: 2019-02-27
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2023-03-15
  Changes: Advisory, Database references, Derived calculations, Other
• Version 1.4: 2024-02-07
  Changes: Data collection, Refinement description