7QBP

Crystal structure of R2-like ligand-binding oxidase from Saccharopolyspora Erythraea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


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 oxidase330Saccharopolyspora erythraea NRRL 2338Mutation(s): 0 
Gene Names: SACE_0591
EC: 1
UniProt
Find proteins for A4F7B2 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338))
Explore A4F7B2 
Go to UniProtKB:  A4F7B2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4F7B2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.173α = 90
b = 103.173β = 90
c = 61.574γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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