6N6P

Crystal structure of [FeFe]-hydrogenase in the presence of 7 mM Sodium dithionite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases.

Artz, J.H.Zadvornyy, O.A.Mulder, D.W.Keable, S.M.Cohen, A.E.Ratzloff, M.W.Williams, S.G.Ginovska, B.Kumar, N.Song, J.McPhillips, S.E.Davidson, C.M.Lyubimov, A.Y.Pence, N.Schut, G.J.Jones, A.K.Soltis, S.M.Adams, M.W.W.Raugei, S.King, P.W.Peters, J.W.

(2020) J Am Chem Soc 142: 1227-1235

  • DOI: 10.1021/jacs.9b08756
  • Primary Citation of Related Structures:  
    6N59, 6N6P, 6NAC

  • PubMed Abstract: 
  • Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur-containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated ...

    Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur-containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated. The microbe Clostridium pasteurianum produces three [FeFe]-hydrogenases that differ in "catalytic bias" by exerting a disproportionate rate acceleration in one direction or the other that spans a remarkable 6 orders of magnitude. The combination of high-resolution structural work, biochemical analyses, and computational modeling indicates that protein secondary interactions directly influence the relative stabilization/destabilization of different oxidation states of the active site metal cluster. This selective stabilization or destabilization of oxidation states can preferentially promote hydrogen oxidation or proton reduction and represents a simple yet elegant model by which a protein catalytic site can confer catalytic bias.


    Organizational Affiliation

    Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Iron hydrogenase 1A574Clostridium 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
402
Query on 402

Download Ideal Coordinates CCD File 
B [auth A]dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 S2
LJPDYWPSPOWMIB-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
G [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.021α = 90
b = 112.021β = 90
c = 103.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0012518

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2020-02-05
    Changes: Database references