6C8R | pdb_00006c8r

Loganic acid O-methyltransferase complexed with SAH and loganic acid

• PDB DOI: https://doi.org/10.2210/pdb6C8R/pdb

• Classification: TRANSFERASE
• Organism(s): Catharanthus roseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-25 Released: 2018-02-07 
• Deposition Author(s): Petronikolou, N., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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

• PubMed: 29399933 
• DOI: https://doi.org/10.1002/cbic.201700679
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Illinois at Urbana-Champaign, Roger Adams Lab Room 430, 600 S. Mathews Avenue, Urbana, IL, 61801, USA.
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
School of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.43 kDa 
• Atom Count: 6,524 
• Modeled Residue Count: 714 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Loganic acid O-methyltransferase	A, B	379	Catharanthus roseus	Mutation(s): 0  EC: 2.1.1.50
UniProt
Find proteins for B2KPR3 (Catharanthus roseus) Explore B2KPR3  Go to UniProtKB:  B2KPR3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
EQV	E [auth B]	Loganic acid C16 H24 O10 JNNGEAWILNVFFD-CDJYTOATSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.44	α = 90
b = 116.233	β = 90
c = 136.679	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Petronikolou, N., Nair, S.K.

Revision History  

• 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