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 

wwPDB Validation 3D Report Full Report


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
  • Also Cited By: 3ZE8, 3ZE7, 3ZEA, 3ZE9, 3ZE6

  • 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 pr ...

    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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
A
317Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: hysB
EC: 1.12.7.2
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72AS4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
B
495Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: hysA
EC: 1.12.7.2
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72AS3
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SBY
Query on SBY

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Download CCD File 
A, B
3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
C17 H37 N O3 S
IZWSFJTYBVKZNK-UHFFFAOYSA-N
 Ligand Interaction
FCO
Query on FCO

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Download CCD File 
B
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FSX
Query on FSX

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A
BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
FE4-S3-O3 CLUSTER
Fe4 O3 S3
BIOGFUMNBIDAOG-VNBKSMEUCR
 Ligand Interaction
FE2
Query on FE2

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B
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PSW
Query on PSW
B
L-PEPTIDE LINKINGC3 H7 N O2 S SeSEC
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.596α = 90.00
b = 91.223β = 101.73
c = 66.751γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXEphasing
XDSdata reduction
XDSdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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