Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 91.44 kDa 
• Atom Count: 6257 
• Modelled Residue Count: 759 
• Deposited Residue Count: 813 
• Unique protein chains: 2

2WPN

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

• DOI: 10.2210/pdb2WPN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio vulgaris str. Hildenborough
• Mutation(s): Yes 


• Deposited: 2009-08-07 Released: 2010-01-12 
• Deposition Author(s): Marques, M.C., Coelho, R., De Lacey, A.L., Pereira, I.A.C., Matias, P.M.

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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 

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

• PubMed: 20026074 
• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT	A	317	Desulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: hysB, DVU_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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING	B	495	Desulfovibrio vulgaris str. Hildenborough	Mutation(s): 1  Gene Names: hysA, DVU_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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSX (Subject of Investigation/LOI)	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
SF4	C [auth A], D [auth A], E [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
SBY (Subject of Investigation/LOI)	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	I [auth B]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI	J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2	K [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CL	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS
PSW	B	L-PEPTIDE LINKING	C3 H7 N O2 S Se		SEC

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 = 60.596	α = 90
b = 91.223	β = 101.73
c = 66.751	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing
SHELXE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2009-08-07 
• Released Date: 2010-01-12 
Deposition Author(s): Marques, M.C., Coelho, R., De Lacey, A.L., Pereira, I.A.C., Matias, P.M.

Revision History  

• 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