5APG

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ribosome Biogenesis Factor Tsr3 is the Aminocarboxypropyl Transferase Responsible for 18S Rrna Hypermodification in Yeast and Humans

Entian, K.-D.Immer, C.Koetter, P.Lafontaine, D.Britter, M.Pogoryelov, D.Sharma, S.Wohnert, J.Wurm, J.P.

(2016) Nucleic Acids Res. 44: 4304

  • DOI: 10.1093/nar/gkw244
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m(1)acp(3)Ψ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionin ...

    The chemically most complex modification in eukaryotic rRNA is the conserved hypermodified nucleotide N1-methyl-N3-aminocarboxypropyl-pseudouridine (m(1)acp(3)Ψ) located next to the P-site tRNA on the small subunit 18S rRNA. While S-adenosylmethionine was identified as the source of the aminocarboxypropyl (acp) group more than 40 years ago the enzyme catalyzing the acp transfer remained elusive. Here we identify the cytoplasmic ribosome biogenesis protein Tsr3 as the responsible enzyme in yeast and human cells. In functionally impaired Tsr3-mutants, a reduced level of acp modification directly correlates with increased 20S pre-rRNA accumulation. The crystal structure of archaeal Tsr3 homologs revealed the same fold as in SPOUT-class RNA-methyltransferases but a distinct SAM binding mode. This unique SAM binding mode explains why Tsr3 transfers the acp and not the methyl group of SAM to its substrate. Structurally, Tsr3 therefore represents a novel class of acp transferase enzymes.


    Organizational Affiliation

    Institute for Molecular Biosciences, Goethe University, Frankfurt/M, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TSR3
A, B, C
185Vulcanisaeta distributa (strain DSM 14429 / JCM 11212 / NBRC 100878 / IC-017)Mutation(s): 0 
Find proteins for E1QU22 (Vulcanisaeta distributa (strain DSM 14429 / JCM 11212 / NBRC 100878 / IC-017))
Go to UniProtKB:  E1QU22
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EEM
Query on EEM

Download SDF File 
Download CCD File 
A, B, C
[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium
Se-ADENOSYLSELENOMETHIONINE
C15 H23 N6 O5 Se
GGJFWMOVUFBSIN-FCKMPRQPSA-O
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.950α = 90.00
b = 66.970β = 89.99
c = 106.420γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references