3H3X

Structure of the V74M large subunit mutant of NI-FE hydrogenase in an oxidized state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Introduction of methionines in the gas channel makes [NiFe] hydrogenase aero-tolerant

Dementin, S.Leroux, F.Cournac, L.de Lacey, A.L.Volbeda, A.Leger, C.Burlat, B.Martinez, N.Champ, S.Martin, L.Sanganas, O.Haumann, M.Fernandez, V.M.Guigliarelli, B.Fontecilla-Camps, J.C.Rousset, M.

(2009) J Am Chem Soc 131: 10156-10164

  • DOI: 10.1021/ja9018258
  • Primary Citation of Related Structures:  
    3H3X

  • PubMed Abstract: 
  • Hydrogenases catalyze the conversion between 2H(+) + 2e(-) and H(2)(1). Most of these enzymes are inhibited by O(2), which represents a major drawback for their use in biotechnological applications. Improving hydrogenase O(2) tolerance is therefore a major contemporary challenge to allow the implementation of a sustainable hydrogen economy ...

    Hydrogenases catalyze the conversion between 2H(+) + 2e(-) and H(2)(1). Most of these enzymes are inhibited by O(2), which represents a major drawback for their use in biotechnological applications. Improving hydrogenase O(2) tolerance is therefore a major contemporary challenge to allow the implementation of a sustainable hydrogen economy. We succeeded in improving O(2) tolerance, which we define here as the ability of the enzyme to resist for several minutes to O(2) exposure, by substituting with methionines small hydrophobic residues strongly conserved in the gas channel. Remarkably, the mutated enzymes remained active in the presence of an O(2) concentration close to that found in aerobic solutions in equilibrium with air, while the wild type enzyme is inhibited in a few seconds. Crystallographic and spectroscopic studies showed that the structure and the chemistry at the active site are not affected by the mutations. Kinetic studies demonstrated that the inactivation is slower and reactivation faster in these mutants. We propose that in addition to restricting O(2) diffusion to the active site of the enzyme, methionine may also interact with bound peroxide and provide an assisted escape route for H(2)O(2) toward the gas channel. These results show for the first time that it is possible to improve O(2)-tolerance of [NiFe] hydrogenases, making possible the development of biohydrogen production systems.


    Related Citations: 
    • Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics
      Montet, Y., Amara, P., Volbeda, A., Vernede, X., Hatchikian, E.C., Field, M.J., Frey, M., Fontecilla-Camps, J.C.
      (1997) Nat Struct Biol 4: 523
    • High-resolution crystallographic analysis of Desulfovibrio fructosovorans [NiFe] hydrogenase
      Volbeda, A., Montet, Y., Vernede, X., Hatchikian, E.C., Fontecilla-Camps, J.C.
      (2002) Int J Hydrogen Energy 27: 1449
    • Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases
      Volbeda, A., Martin, L., Cavazza, C., Matho, M., Faber, B.W., Roseboom, W., Albracht, S.P., Garcin, E., Rousset, M., Fontecilla-Camps, J.C.
      (2005) J Biol Inorg Chem 10: 239
    • Experimental approaches to kinetics of gas diffusion in hydrogenase
      Leroux, F., Dementin, S., Burlat, B., Cournac, L., Volbeda, A., Champ, S., Martin, L., Guigliarelli, B., Bertrand, P., Fontecilla-Camps, J.C., Rousset, M.
      (2008) Proc Natl Acad Sci U S A 105: 11188

    Organizational Affiliation

    CNRS, Bioénergétique et Ingénierie des Protéines, IMM, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA, C [auth B], E [auth C]264Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
UniProt
Find proteins for P18187 (Desulfovibrio fructosivorans)
Explore P18187 
Go to UniProtKB:  P18187
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [auth Q], D [auth R], F [auth S]549Desulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydB
EC: 1.12.2.1
UniProt
Find proteins for P18188 (Desulfovibrio fructosivorans)
Explore P18188 
Go to UniProtKB:  P18188
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 Ideal Coordinates CCD File 
AA [auth C], G [auth A], I [auth A], P [auth B], R [auth B], Y [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
H [auth A], Q [auth B], Z [auth C]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
BA [auth S], K [auth Q], S [auth R]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth S], J [auth A], N [auth Q], O [auth Q], V [auth R], W [auth R], X [auth R]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
CA [auth S], L [auth Q], T [auth R]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth S], M [auth Q], U [auth R]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.4α = 90
b = 99.2β = 92.8
c = 182.3γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-03-07
    Changes: Data collection