2WPN

Structure of the oxidised, as-isolated NiFeSe hydrogenase from D. vulgaris Hildenborough


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

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This is version 2.1 of the entry. See complete history


Literature

The three-dimensional structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough: a hydrogenase without a bridging ligand in the active site in its oxidised, "as-isolated" state.

Marques, M.C.Coelho, R.De Lacey, A.L.Pereira, I.A.Matias, P.M.

(2010) J Mol Biol 396: 893-907

  • DOI: https://doi.org/10.1016/j.jmb.2009.12.013
  • Primary Citation of Related Structures:  
    2WPN

  • PubMed Abstract: 

    Hydrogen is a good energy vector, and its production from renewable sources is a requirement for its widespread use. [NiFeSe] hydrogenases (Hases) are attractive candidates for the biological production of hydrogen because they are capable of high production rates even in the presence of moderate amounts of O(2), lessening the requirements for anaerobic conditions. The three-dimensional structure of the [NiFeSe] Hase from Desulfovibrio vulgaris Hildenborough has been determined in its oxidised "as-isolated" form at 2.04-A resolution. Remarkably, this is the first structure of an oxidised Hase of the [NiFe] family that does not contain an oxide bridging ligand at the active site. Instead, an extra sulfur atom is observed binding Ni and Se, leading to a SeCys conformation that shields the NiFe site from contact with oxygen. This structure provides several insights that may explain the fast activation and O(2) tolerance of these enzymes.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT317Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
EC: 1.18.99.1
UniProt
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS4 
Go to UniProtKB:  Q72AS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING495Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 1 
EC: 1.18.99.1
UniProt
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS3 
Go to UniProtKB:  Q72AS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FSX
Query on FSX

Download Ideal Coordinates CCD File 
F [auth A]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-UHFFFAOYSA-M
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SBY
Query on SBY

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G [auth A],
H [auth A],
M [auth B],
N [auth B]
3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
C17 H37 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-N
FCO
Query on FCO

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I [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI
Query on NI

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J [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2
Query on FE2

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K [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
PSW
Query on PSW
B
L-PEPTIDE LINKINGC3 H7 N O2 S SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.596α = 90
b = 91.223β = 101.73
c = 66.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other
  • Version 1.3: 2014-11-05
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.0: 2019-04-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Polymer sequence, Structure summary
  • Version 2.1: 2019-07-10
    Changes: Advisory, Data collection