7QBK

Crystal structure of a second homolog of R2-like ligand-binding oxidase in Sulfolobus acidocaldarius (SaR2loxII)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase.

Diamanti, R.Srinivas, V.Johansson, A.I.Nordstrom, A.Griese, J.J.Lebrette, H.Hogbom, M.

(2022) FEBS Lett 596: 1600-1610

  • DOI: https://doi.org/10.1002/1873-3468.14319
  • Primary Citation of Related Structures:  
    7QBK, 7QBP

  • PubMed Abstract: 

    R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese-iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine-valine ether cross-link in the protein scaffold upon O 2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius322Sulfolobus acidocaldarius DSM 639Mutation(s): 0 
Gene Names: Saci_1112
UniProt
Find proteins for Q4J9R6 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Explore Q4J9R6 
Go to UniProtKB:  Q4J9R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4J9R6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.029α = 90
b = 128.029β = 90
c = 41.894γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)SwedenHIGH-GEAR 724394
Swedish Research CouncilSweden2017-04018
Knut and Alice Wallenberg FoundationSweden2017.0275
Knut and Alice Wallenberg FoundationSweden2019.0436

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description