4C3O

Structure and function of an oxygen tolerant NiFe hydrogenase from Salmonella

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 

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
  • Primary Citation of Related Structures:  
    4C3O

  • 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 was determined to a resolution of 3 ...

    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 Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, U.K.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASE-1 LARGE SUBUNITA, C, E585Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: STM1538
EC: 1.12.7.2
UniProt
Find proteins for Q8ZPH0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZPH0 
Go to UniProtKB:  Q8ZPH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZPH0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASE-1 SMALL SUBUNITB, D, F279Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: STM1539
EC: 1.12.7.2 (PDB Primary Data), 1.12.99.6 (UniProt)
UniProt
Find proteins for Q8ZPG9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZPG9 
Go to UniProtKB:  Q8ZPG9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZPG9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
AA [auth F],
M [auth B],
S [auth D]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F4S
Query on F4S
Download Ideal Coordinates CCD File 
O [auth B],
U [auth D],
Z [auth F]		FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
BA [auth F],
N [auth B],
T [auth D]		FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
NFU
Query on NFU
Download Ideal Coordinates CCD File 
G [auth A],
Q [auth C],
V [auth E]		formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
C3 H Fe N2 Ni O
QCZROEOIPZWDEO-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
CA [auth F],
P [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
W [auth E],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
W [auth E],
X [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
L [auth A],
R [auth C],
Y [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.46α = 90
b = 122.21β = 95.56
c = 227.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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