9FN2 | pdb_00009fn2

Crystal structure of the alkyltransferase ribozyme SAMURI co-crystallized with SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.230 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI.

Chen, H.A.Okuda, T.Lenz, A.K.Scheitl, C.P.M.Schindelin, H.Hobartner, C.

(2025) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-024-01808-w
  • Primary Citation of Related Structures:  
    9FN2, 9FN3

  • PubMed Abstract: 

    Ribozymes that catalyze site-specific RNA modification have recently gained increasing interest for their ability to mimic methyltransferase enzymes and for their application to install molecular tags. Recently, we reported SAMURI as a site-specific alkyltransferase ribozyme using S-adenosylmethionine (SAM) or a stabilized analog to transfer a methyl or propargyl group to N 3 of an adenosine. Here, we report the crystal structures of SAMURI in the postcatalytic state. The structures reveal a three-helix junction with the catalytic core folded into four stacked layers, harboring the cofactor and the modified nucleotide. Detailed structure-activity analyses explain the cofactor scope and the structural basis for site selectivity. A structural comparison of SAMURI with SAM riboswitches sheds light on how the synthetic ribozyme overcomes the strategies of natural riboswitches to avoid self-methylation. Our results suggest that SAM and its analogs may serve as substrates for various RNA-catalyzed reactions, for which the corresponding ribozymes remain to be identified.


  • Organizational Affiliation
    • Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.

Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
SAMURI-SAM
A, B
58synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.230 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.444α = 90
b = 75.444β = 90
c = 73.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 2.0: 2025-02-05
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description