5OEF | pdb_00005oef

Active semisynthetic [FeFe]-hydrogenase CpI with aza-diselenato-bridged [2Fe] cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Chalcogenide substitution in the [2Fe] cluster of [FeFe]-hydrogenases conserves high enzymatic activity.

Kertess, L.Wittkamp, F.Sommer, C.Esselborn, J.Rudiger, O.Reijerse, E.J.Hofmann, E.Lubitz, W.Winkler, M.Happe, T.Apfel, U.P.

(2017) Dalton Trans 46: 16947-16958

  • DOI: https://doi.org/10.1039/c7dt03785f
  • Primary Citation Related Structures: 
    5OEF

  • PubMed Abstract: 

    [FeFe]-Hydrogenases efficiently catalyze the uptake and evolution of H 2 due to the presence of an inorganic [6Fe-6S]-cofactor (H-cluster). This cofactor is comprised of a [4Fe-4S] cluster coupled to a unique [2Fe] cluster where the catalytic turnover of H 2 /H + takes place. We herein report on the synthesis of a selenium substituted [2Fe] cluster [Fe 2 {μ(SeCH 2 ) 2 NH}(CO) 4 (CN) 2 ] 2- (ADSe) and its successful in vitro integration into the native protein scaffold of [FeFe]-hydrogenases HydA1 from Chlamydomonas reinhardtii and CpI from Clostridium pasteurianum yielding fully active enzymes (HydA1-ADSe and CpI-ADSe). FT-IR spectroscopy and X-ray structure analysis confirmed the presence of structurally intact ADSe at the active site. Electrochemical assays reveal that the selenium containing enzymes are more biased towards hydrogen production than their native counterparts. In contrast to previous chalcogenide exchange studies, the S to Se exchange herein is not based on a simple reconstitution approach using ionic cluster constituents but on the in vitro maturation with a pre-synthesized selenium-containing [2Fe] mimic. The combination of biological and chemical methods allowed for the creation of a novel [FeFe]-hydrogenase with a [2Fe2Se]-active site which confers individual catalytic features.


  • Organizational Affiliation
    • Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Universitätsstraße 150, 44801 Bochum, Germany. Thomas.Happe@rub.de.

Macromolecule Content 

  • Total Structure Weight: 134.41 kDa 
  • Atom Count: 9,760 
  • Modeled Residue Count: 1,147 
  • Deposited Residue Count: 1,168 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron hydrogenase 1
A, B
584Clostridium pasteurianumMutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum)
Explore P29166 
Go to UniProtKB:  P29166
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29166
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9SQ
(Subject of Investigation/LOI)

Query on 9SQ



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethaneselenato- 1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 Se2
PHBGCQLNCRESHS-UHFFFAOYSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
L [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
H [auth A],
P [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
Q [auth B],
R [auth B],
S [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.35α = 90
b = 72.88β = 98.7
c = 103.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEXC1069

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description