5JSU

The 3D structure of the U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough in the oxidized state at 1.40 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 

wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing507Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 1 
Gene Names: hysADVU_1918
EC: 1.12.7.2
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 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6ML
Query on 6ML

Download Ideal Coordinates CCD File 
F [auth A]oxygen-damaged SF4
Fe4 O2 S4
DCVJTSMMUVGUAG-UHFFFAOYSA-M
SF4
Query on SF4

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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
NI
Query on NI

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

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J [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
H2S
Query on H2S

Download Ideal Coordinates CCD File 
H [auth B],
K [auth B]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
CSX
Query on CSX
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.204α = 90
b = 62.655β = 104.97
c = 109.841γ = 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: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Derived calculations