8BJ8

Desulfovibrio desulfuricans FeFe Hydrogenase C178A mutant in Htrans-like state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of exogenous cyanide reveals new active-site states in [FeFe] hydrogenases.

Martini, M.A.Bikbaev, K.Pang, Y.Lorent, C.Wiemann, C.Breuer, N.Zebger, I.DeBeer, S.Span, I.Bjornsson, R.Birrell, J.A.Rodriguez-Macia, P.

(2023) Chem Sci 14: 2826-2838

  • DOI: https://doi.org/10.1039/d2sc06098a
  • Primary Citation of Related Structures:  
    8BJ7, 8BJ8

  • PubMed Abstract: 

    [FeFe] hydrogenases are highly efficient metalloenyzmes for hydrogen conversion. Their active site cofactor (the H-cluster) is composed of a canonical [4Fe-4S] cluster ([4Fe-4S] H ) linked to a unique organometallic di-iron subcluster ([2Fe] H ). In [2Fe] H the two Fe ions are coordinated by a bridging 2-azapropane-1,3-dithiolate (ADT) ligand, three CO and two CN - ligands, leaving an open coordination site on one Fe where substrates (H 2 and H + ) as well as inhibitors ( e.g. O 2 , CO, H 2 S) may bind. Here, we investigate two new active site states that accumulate in [FeFe] hydrogenase variants where the cysteine (Cys) in the proton transfer pathway is mutated to alanine (Ala). Our experimental data, including atomic resolution crystal structures and supported by calculations, suggest that in these two states a third CN - ligand is bound to the apical position of [2Fe] H . These states can be generated both by "cannibalization" of CN - from damaged [2Fe] H subclusters as well as by addition of exogenous CN - . This is the first detailed spectroscopic and computational characterisation of the interaction of exogenous CN - with [FeFe] hydrogenases. Similar CN - -bound states can also be generated in wild-type hydrogenases, but do not form as readily as with the Cys to Ala variants. These results highlight how the interaction between the first amino acid in the proton transfer pathway and the active site tunes ligand binding to the open coordination site and affects the electronic structure of the H-cluster.


  • Organizational Affiliation

    Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany maria.martini@cec.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [Fe] hydrogenase large subunit396Desulfovibrio desulfuricansMutation(s): 1 
Gene Names: hydADVU_1769
EC: 1.12.7.2
UniProt
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07598 
Go to UniProtKB:  P07598
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07598
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [Fe] hydrogenase small subunit88Desulfovibrio desulfuricansMutation(s): 0 
Gene Names: hydBDVU_1770
EC: 1.12.7.2
UniProt
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07603 
Go to UniProtKB:  P07603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07603
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.387α = 90
b = 87.411β = 90
c = 89.125γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySP 1476/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2024-02-07
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Database references