3CUR

Structure of a double methionine mutant of NI-FE hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.Rousset, M.

(2008) Proc.Natl.Acad.Sci.Usa 105: 11188-11193

  • DOI: 10.1073/pnas.0803689105
  • Primary Citation of Related Structures:  
  • Also Cited By: 3H3X

  • PubMed Abstract: 
  • Hydrogenases, which catalyze H(2) to H(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. Howe ...

    Hydrogenases, which catalyze H(2) to H(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H(2) toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these.


    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.Mol.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


    Organizational Affiliation

    Centre National de la Recherche Scientifique, Institut de Biologie Structurale et Microbiologie, Unité Propre de Recherche 9036, Unité de Bioénergétique et Ingénierie des Protéines, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase small subunit
A, B, C
264Desulfovibrio fructosivoransMutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P18187 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18187
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase large subunit
H, I, J
549Desulfovibrio fructosivoransMutation(s): 2 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P18188 (Desulfovibrio fructosivorans)
Go to UniProtKB:  P18188
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
A, B, C
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

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Download CCD File 
H, I, J
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
H, I, J
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PER
Query on PER

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H, I, J
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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H, I, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
H, I, J
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.600α = 90.00
b = 99.900β = 91.60
c = 183.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
ADSCdata collection
XDSdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-04-17 
  • Released Date: 2008-08-05 
  • Deposition Author(s): Volbeda, A.

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-09-07
    Type: Database references