4UD2

Structure of anaerobically purified D. fructosovorans NiFe- hydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

[Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in a Variant with Accrued O2-Tolerance and a Tentative Re-Interpretation of Ni-Si States.

Volbeda, A.Martin, L.Liebgott, P.-P.De Lacey, A.L.Fontecilla-Camps, J.C.

(2015) Metallomics 7: 710

  • DOI: 10.1039/c4mt00309h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • [NiFe]-hydrogenases are well-studied enzymes capable of oxidizing molecular hydrogen and reducing protons. EPR and FTIR spectroscopic studies have shown that these enzymes can be isolated in several redox states that include paramagnetic oxidized ina ...

    [NiFe]-hydrogenases are well-studied enzymes capable of oxidizing molecular hydrogen and reducing protons. EPR and FTIR spectroscopic studies have shown that these enzymes can be isolated in several redox states that include paramagnetic oxidized inactive Ni-A and Ni-B species and a reduced Ni-C form. The latter and the diamagnetic respectively more oxidized Ni-SI and more reduced Ni-R forms are generally thought to be involved in the catalytic cycle of [NiFe]-hydrogenases. With the exception of Ni-SI, these different stable states have been well characterized. Here, based on the crystal structure of a partially reduced Desulfovibrio fructosovorans (Df) enzyme and data from the literature we propose that at least one of the Ni-SI sub-states contains an unexpected combination of hydride and sulfenic acid moieties. We have also determined the structure of the less oxygen-sensitive Df [NiFe]-hydrogenase V74C mutant and found that more than half of the active site nickel occupies a novel position, called Ni'. In this new position, the metal ion is coordinated by two cysteine thiolates, a bridging species modeled as SH(-) and a main chain carboxamido N atom. The Ni' coordination is similar to the one found in Ni superoxide dismutase, an enzyme that operates at significantly more positive potentials than [NiFe]-hydrogenases. We propose that the oxygen-tolerance of the V74C variant results from a high potential stabilization of a Ni'(iii) species induced by the change in the metal ion coordination sphere. We also propose that transient Ni'(iii) species can rapidly attract successive electrons from the Fe4S4 proximal cluster accelerating the reduction of oxygen to water and hydroxide. The naturally occurring oxygen-tolerant [NiFe]-hydrogenases have an unusual proximal cluster that has been shown to be exceptionally plastic and capable of undergoing two successive one-electron oxidations. This double oxidation is modulated by the migration of one of the iron atoms in the cluster to the main chain where, as Fe(iii), it forms a bond with a carboxamido N ligand. Like in the Df V74C variant the electrons from the proximal cluster help reducing O2 to H2O and OH(-). In conclusion, in both cases a metal-carboxamido bond may explain, at least partially, the observed oxygen tolerance.


    Organizational Affiliation

    CEA, IBS, F-38044 Grenoble, France. anne.volbeda@ibs.fr juan.fontecilla@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
A, B, C
264Desulfovibrio fructosivorans JJMutation(s): 0 
EC: 1.12.2.1
Find proteins for E1K248 (Desulfovibrio fructosivorans JJ)
Go to UniProtKB:  E1K248
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
Q, R, S
549Desulfovibrio fructosivorans JJMutation(s): 0 
Find proteins for E1K247 (Desulfovibrio fructosivorans JJ)
Go to UniProtKB:  E1K247
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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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 
Q, R, S
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, Q, R, S
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Q, R, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Q, R, S
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
Q, R, S
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.010α = 90.00
b = 100.170β = 91.42
c = 183.980γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
AMoREphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Derived calculations, Experimental preparation, Other