1E3D

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Observed: 0.167 

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This is version 2.0 of the entry. See complete history. 


Literature

[Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with the Tetrahaem Cytochrome C3.

Matias, P.M., Soares, C.M., Saraiva, L.M., Coelho, R., Morais, J., Le Gall, J., Carrondo, M.A.

(2001) J Biol Inorg Chem 6: 63-81

  • DOI: 10.1007/s007750000167
  • Primary Citation of Related Structures:  
    1E3D

  • PubMed Abstract: 

    • The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfitricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and Rfree=0 ...

    The primary and three-dimensional structures of a [NiFe] hydrogenase isolated from D. desulfitricans ATCC 27774 were determined, by nucleotide analysis and single-crystal X-ray crystallography. The three-dimensional structural model was refined to R=0.167 and Rfree=0.223 using data to 1.8 A resolution. Two unique structural features are observed: the [4Fe-4S] cluster nearest the [NiFe] centre has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms; a three-fold disorder was observed for Cys536 which binds to the nickel atom in the [NiFe] centre. Also, the bridging sulfur atom that caps the active site was found to have partial occupancy, thus corresponding to a partly activated enzyme. These structural features may have biological relevance. In particular, the two less-populated rotamers of Cys536 may be involved in the activation process of the enzyme, as well as in the catalytic cycle. Molecular modelling studies were carried out on the interaction between this [NiFe] hydrogenase and its physiological partner, the tetrahaem cytochrome c3 from the same organism. The lowest energy docking solutions were found to correspond to an interaction between the haem IV region in tetrahaem cytochrome c3 with the distal [4Fe-4S] cluster in [NiFe] hydrogenase. This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres and the fact that electron transfer decay coupling calculations show high coupling values and a short electron transfer pathway. On the other hand, other docking solutions have been found that, despite showing low electron transfer efficiency, may give clues on possible proton transfer mechanisms between the two molecules.

    Organizational Affiliation: 

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
[NiFe] hydrogenase small subunitA, C266Desulfovibrio desulfuricansMutation(s): 0 
EC: 1.12.2.1
Find proteins for Q9L869 (Desulfovibrio desulfuricans)
Explore Q9L869 
Go to UniProtKB:  Q9L869
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
[NiFe] hydrogenase large subunitB, D542Desulfovibrio desulfuricansMutation(s): 0 
Find proteins for Q9L868 (Desulfovibrio desulfuricans)
Explore Q9L868 
Go to UniProtKB:  Q9L868
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSX
Query on FSX
Download Ideal Coordinates CCD File 
 G [auth A], N [auth C]BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
Fe4 O3 S3
BIOGFUMNBIDAOG-VNBKSMEUCR		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
 F [auth A], M [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
 E [auth A], L [auth C]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
FNE
Query on FNE
Download Ideal Coordinates CCD File 
 I [auth B], P [auth D](MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
C3 Fe Ni O3 S
RSNJUOPWNIKDNA-LMILJAESAR		 Ligand Interaction
H2S
Query on H2S
Download Ideal Coordinates CCD File 
 H [auth A], K [auth B], O [auth C], R [auth D]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
 J [auth B], Q [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.09α = 90
b = 169.98β = 92.8
c = 72.62γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-06-13
    Changes: Advisory, Atomic model, Data collection, Database references, Source and taxonomy, Structure summary