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: 1.4 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nchembio.2335
  • Primary Citation of Related Structures:  

  • 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 H2 production. In contrast to [NiFe] hydrogena ...

    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 H2 production. In contrast to [NiFe] hydrogenases, they display reduced H2 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: 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
507Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 1 
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 6 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
FCO
Query on FCO

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Download CCD File 
B
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

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Download CCD File 
B
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
6ML
Query on 6ML

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Download CCD File 
A
oxygen-damaged SF4
Fe4 O2 S4
DCVJTSMMUVGUAG-UHFFFAOYSA-M
 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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Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
CSD
Query on CSD
B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.110 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.204α = 90.00
b = 62.655β = 104.97
c = 109.841γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references