3H3X | pdb_00003h3x

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 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3H3X

This is version 1.5 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: https://doi.org/10.1021/ja9018258
  • Primary Citation 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. 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.


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

Macromolecule Content 

  • Total Structure Weight: 268.75 kDa 
  • Atom Count: 19,100 
  • Modeled Residue Count: 2,417 
  • Deposited Residue Count: 2,439 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA,
C [auth B],
E [auth C]
264Solidesulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
UniProt
Find proteins for P18187 (Solidesulfovibrio fructosivorans)
Explore P18187 
Go to UniProtKB:  P18187
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18187
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [auth Q],
D [auth R],
F [auth S]
549Solidesulfovibrio fructosivoransMutation(s): 1 
Gene Names: hydB
EC: 1.12.2.1
UniProt
Find proteins for P18188 (Solidesulfovibrio fructosivorans)
Explore P18188 
Go to UniProtKB:  P18188
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18188
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / 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]
AA [auth C],
G [auth A],
I [auth A],
P [auth B],
R [auth B],
Y [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S

Query on F3S



Download:Ideal Coordinates CCD File
H [auth A],
Q [auth B],
Z [auth C]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
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
GOL

Query on GOL



Download:Ideal Coordinates CCD File
EA [auth S]
J [auth A]
N [auth Q]
O [auth Q]
V [auth R]
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
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
MG

Query on MG



Download:Ideal Coordinates CCD File
DA [auth S],
M [auth Q],
U [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
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
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary