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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Ligand Structure Quality Assessment 


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: 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 ...

    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.


    Related Citations: 
    • Purification, Crystallization and Preliminary Crystallographic Analysis of the [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough.
      Marques, M., Coelho, R., Pereira, I.A., Matias, P.M.
      (2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 920

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNITA317Desulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: hysBDVU_1917
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS4 
Go to UniProtKB:  Q72AS4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAININGB495Desulfovibrio vulgaris str. HildenboroughMutation(s): 1 
Gene Names: hysADVU_1918
EC: 1.18.99.1 (PDB Primary Data), 1.12.7.2 (UniProt)
UniProt
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS3 
Go to UniProtKB:  Q72AS3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSX (Subject of Investigation/LOI)
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-VNBKSMEUCR
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SBY (Subject of Investigation/LOI)
Query on SBY

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
I [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
J [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
K [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
BL-PEPTIDE LINKINGC3 H7 N O5 SCYS
PSW
Query on PSW
BL-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