4C3O

Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

How the Structure of the Large Subunit Controls Function in an Oxygen-Tolerant [Nife]-Hydrogenase.

Bowman, L.Flanagan, L.Fyfe, P.K.Parkin, A.Hunter, W.N.Sargent, F.

(2014) Biochem.J. 458: 449

  • DOI: 10.1042/BJ20131520

  • PubMed Abstract: 
  • Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure w ...

    Salmonella enterica is an opportunistic pathogen that produces a [NiFe]-hydrogenase under aerobic conditions. In the present study, genetic engineering approaches were used to facilitate isolation of this enzyme, termed Hyd-5. The crystal structure was determined to a resolution of 3.2 Å and the hydro-genase was observed to comprise associated large and small subunits. The structure indicated that His229 from the large subunit was close to the proximal [4Fe-3S] cluster in the small subunit. In addition, His229 was observed to lie close to a buried glutamic acid (Glu73), which is conserved in oxygen-tolerant hydrogenases. His229 and Glu73 of the Hyd-5 large subunit were found to be important in both hydrogen oxidation activity and the oxygen-tolerance mechanism. Substitution of His229 or Glu73 with alanine led to a loss in the ability of Hyd-5 to oxidize hydrogen in air. Furthermore, the H229A variant was found to have lost the overpotential requirement for activity that is always observed with oxygen-tolerant [NiFe]-hydrogenases. It is possible that His229 has a role in stabilizing the super-oxidized form of the proximal cluster in the presence of oxygen, and it is proposed that Glu73could play a supporting role in fine-tuning the chemistry of His229 to enable this function.


    Related Citations: 
    • How Salmonella Oxidises H(2) Under Aerobic Conditions.
      Parkin, A.,Bowman, L.,Roessler, M.M.,Davies, R.A.,Palmer, T.,Armstrong, F.A.,Sargent, F.
      (2012) FEBS Lett. 586: 536


    Organizational Affiliation

    ‡Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.,*Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.,†Department of Chemistry, University of York, Heslington, York YO10 5DD, England, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE-1 LARGE SUBUNIT
A, C, E
585Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
EC: 1.12.7.2
Find proteins for Q8ZPH0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZPH0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE-1 SMALL SUBUNIT
B, D, F
279Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
EC: 1.12.7.2
Find proteins for Q8ZPG9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZPG9
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download SDF File 
Download CCD File 
B, D, F
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NFU
Query on NFU

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Download CCD File 
A, C, E
formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
NI-FE REDUCED ACTIVE CENTER
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
F4S
Query on F4S

Download SDF File 
Download CCD File 
B, D, F
FE4-S3 CLUSTER
T-CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.460α = 90.00
b = 122.210β = 95.56
c = 227.820γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Source and taxonomy
  • Version 2.0: 2018-06-27
    Type: Atomic model, Data collection, Derived calculations