6C8R

Loganic acid O-methyltransferase complexed with SAH and loganic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

Loganic Acid Methyltransferase: Insights into the Specificity of Methylation on an Iridoid Glycoside.

Petronikolou, N., Hollatz, A.J., Schuler, M.A., Nair, S.K.

(2018) Chembiochem 19: 784-788

  • DOI: https://doi.org/10.1002/cbic.201700679
  • Primary Citation of Related Structures:  
    6C8R, 6C8S

  • PubMed Abstract: 

    Loganin is an iridoid glycoside of interest as both an intermediate in the biosynthesis of indole alkaloids in plants and as a bioactive compound itself. Loganic acid methyltransferase catalyzes the methylation of a monoterpenoid glycoside precursor to produce loganin and demonstrates stereospecificity for the (6S,7R) substrate. We have biochemically characterized this biocatalyst and elucidated the basis for its strict substrate specificity. These studies could help facilitate the design of new classes of monoterpenoid indole alkaloids of pharmaceutical interest.

    • Organizational Affiliation: 

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Roger Adams Lab Room 430, 600 S. Mathews Avenue, Urbana, IL, 61801, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Loganic acid O-methyltransferase
A, B
379Catharanthus roseusMutation(s): 0 
UniProt
Find proteins for B2KPR3 (Catharanthus roseus)
Explore B2KPR3 
Go to UniProtKB:  B2KPR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2KPR3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.44α = 90
b = 116.233β = 90
c = 136.679γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description