R2-like ligand-binding oxidase A171F mutant with aerobically reconstituted Mn/Fe cofactor

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine-valine ether cross-link formation in the R2-like ligand-binding oxidase.

Griese, J.J.Kositzki, R.Haumann, M.Hogbom, M.

(2019) J Biol Inorg Chem 24: 211-221

  • DOI: https://doi.org/10.1007/s00775-019-01639-4
  • Primary Citation of Related Structures:  
    6F65, 6F6B, 6F6L, 6F6M

  • PubMed Abstract: 

    R2-like ligand-binding oxidases (R2lox) assemble a heterodinuclear Mn/Fe cofactor which performs reductive dioxygen (O 2 ) activation, catalyzes formation of a tyrosine-valine ether cross-link in the protein scaffold, and binds a fatty acid in a putative substrate channel. We have previously shown that the N-terminal metal binding site 1 is unspecific for manganese or iron in the absence of O 2 , but prefers manganese in the presence of O 2 , whereas the C-terminal site 2 is specific for iron. Here, we analyze the effects of amino acid exchanges in the cofactor environment on cofactor assembly and metalation specificity using X-ray crystallography, X-ray absorption spectroscopy, and metal quantification. We find that exchange of either the cross-linking tyrosine or the valine, regardless of whether the mutation still allows cross-link formation or not, results in unspecific manganese or iron binding at site 1 both in the absence or presence of O 2 , while site 2 still prefers iron as in the wild-type. In contrast, a mutation that blocks binding of the fatty acid does not affect the metal specificity of either site under anoxic or aerobic conditions, and cross-link formation is still observed. All variants assemble a dinuclear trivalent metal cofactor in the aerobic resting state, independently of cross-link formation. These findings imply that the cross-link residues are required to achieve the preference for manganese in site 1 in the presence of O 2 . The metalation specificity, therefore, appears to be established during the redox reactions leading to cross-link formation.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. julia.griese@icm.uu.se.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleotide reductase small subunit316Geobacillus kaustophilus HTA426Mutation(s): 1 
Gene Names: GK2771
Find proteins for Q5KW80 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KW80 
Go to UniProtKB:  Q5KW80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KW80
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.966α = 90
b = 97.196β = 90
c = 128.233γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description