7NTN

The structure of RRM domain of human TRMT2A at 2 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death.

Margreiter, M.A.Witzenberger, M.Wasser, Y.Davydova, E.Janowski, R.Metz, J.Habib, P.Sahnoun, S.E.M.Sobisch, C.Poma, B.Palomino-Hernandez, O.Wagner, M.Carell, T.Jon Shah, N.Schulz, J.B.Niessing, D.Voigt, A.Rossetti, G.

(2022) Comput Struct Biotechnol J 20: 443-458

  • DOI: https://doi.org/10.1016/j.csbj.2021.12.029
  • Primary Citation of Related Structures:  
    7NTN, 7NTO

  • PubMed Abstract: 

    Polyglutamine (polyQ) diseases are characterized by an expansion of cytosine-adenine-guanine (CAG) trinucleotide repeats encoding for an uninterrupted prolonged polyQ tract. We previously identified TRMT2A as a strong modifier of polyQ-induced toxicity in an unbiased large-scale screen in Drosophila melanogaster . This work aimed at identifying and validating pharmacological TRMT2A inhibitors as treatment opportunities for polyQ diseases in humans. Computer-aided drug discovery was implemented to identify human TRMT2A inhibitors. Additionally, the crystal structure of one protein domain, the RNA recognition motif (RRM), was determined, and Biacore experiments with the RRM were performed. The identified molecules were validated for their potency to reduce polyQ aggregation and polyQ-induced cell death in human HEK293T cells and patient derived fibroblasts. Our work provides a first step towards pharmacological inhibition of this enzyme and indicates TRMT2A as a viable drug target for polyQ diseases.


  • Organizational Affiliation

    Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Juelich GmbH, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (uracil-5-)-methyltransferase homolog A81Homo sapiensMutation(s): 0 
Gene Names: TRMT2AHTF9C
EC: 2.1.1 (PDB Primary Data), 2.1.1.35 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZ69 (Homo sapiens)
Explore Q8IZ69 
Go to UniProtKB:  Q8IZ69
PHAROS:  Q8IZ69
GTEx:  ENSG00000099899 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IZ69
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.45α = 90
b = 131.45β = 90
c = 131.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Data collection