7V9E

Crystal structure of a methyl transferase ribozyme

  • Classification: RNA
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-08-25 Released: 2022-03-23 
  • Deposition Author(s): Deng, J., Lilley, D.M.J., Huang, L.
  • Funding Organization(s): Ministry of Education (MoE, China), Cancer Research UK

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of a methyltransferase ribozyme.

Deng, J.Wilson, T.J.Wang, J.Peng, X.Li, M.Lin, X.Liao, W.Lilley, D.M.J.Huang, L.

(2022) Nat Chem Biol 18: 556-564

  • DOI: https://doi.org/10.1038/s41589-022-00982-z
  • Primary Citation of Related Structures:  
    7V9E

  • PubMed Abstract: 

    Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 Å, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry.


  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (68-MER)68Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GUN (Subject of Investigation/LOI)
Query on GUN

Download Ideal Coordinates CCD File 
B [auth A]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
BA
Query on BA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.381α = 90
b = 52.507β = 90
c = 99.939γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
ADDREFdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, China)United Kingdom--
Cancer Research UKUnited KingdomA18604

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references
  • Version 1.2: 2022-05-11
    Changes: Database references
  • Version 1.3: 2024-05-29
    Changes: Data collection