5JSK | pdb_00005jsk

The 3D structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the reduced state at 0.95 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 
    0.120 (Depositor), 0.122 (DCC) 
  • R-Value Work: 
    0.110 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 
    0.111 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis.

Marques, M.C.Tapia, C.Gutierrez-Sanz, O.Ramos, A.R.Keller, K.L.Wall, J.D.De Lacey, A.L.Matias, P.M.Pereira, I.A.C.

(2017) Nat Chem Biol 13: 544-550

  • DOI: https://doi.org/10.1038/nchembio.2335
  • Primary Citation Related Structures: 
    5JSH, 5JSK, 5JSU, 5JSY, 5JT1

  • PubMed Abstract: 

    Hydrogenases are highly active enzymes for hydrogen production and oxidation. [NiFeSe] hydrogenases, in which selenocysteine is a ligand to the active site Ni, have high catalytic activity and a bias for H 2 production. In contrast to [NiFe] hydrogenases, they display reduced H 2 inhibition and are rapidly reactivated after contact with oxygen. Here we report an expression system for production of recombinant [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough and study of a selenocysteine-to-cysteine variant (Sec489Cys) in which, for the first time, a [NiFeSe] hydrogenase was converted to a [NiFe] type. This modification led to severely reduced Ni incorporation, revealing the direct involvement of this residue in the maturation process. The Ni-depleted protein could be partly reconstituted to generate an enzyme showing much lower activity and inactive states characteristic of [NiFe] hydrogenases. The Ni-Sec489Cys variant shows that selenium has a crucial role in protection against oxidative damage and the high catalytic activities of the [NiFeSe] hydrogenases.


  • Organizational Affiliation
    • Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.

Macromolecule Content 

  • Total Structure Weight: 91.48 kDa 
  • Atom Count: 7,112 
  • Modeled Residue Count: 765 
  • Deposited Residue Count: 824 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase, small subunit317Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: hysBDVU_1917
EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS4 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing507Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: hysADVU_1918
EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / 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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
FCO

Query on FCO



Download:Ideal Coordinates CCD File
G [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
F [auth B],
H [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
I [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
H2S

Query on H2S



Download:Ideal Coordinates CCD File
J [auth B]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free:  0.120 (Depositor), 0.122 (DCC) 
  • R-Value Work:  0.110 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 0.111 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.28α = 90
b = 62.77β = 105.11
c = 110.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e TecnologiaPortugalPTDC/BBB-BEP/0934/2012
Fundacao para a Ciencia e TecnologiaPortugalPEst OE/EQB/LA0004/2011
Fundacao para a Ciencia e TecnologiaPortugalSFRH/BD/60879/2009

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-05-03
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary