Modomics - A Database of RNA Modifications

ID Card:

Full name: Dimethyladenosine transferase
Synonym: Dim1
GI: 1169344
Orf: YPL266W
COG: COG0030
UniProt: P41819
Structures: | 6RBD | 6ZQD | 6ZQE | 6ZQF | 6ZQG | 7AJU |
Alpha Fold Predicted Structure: AF-P41819-F1
Enzyme type: methyltransferase
Position of modification - modification: s:1779(1518) - m6,6A
s:1780(1519) - m6,6A


PDB Structures:


6RBD

Structure Description:

Title: State 1 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles
Classification: RIBOSOME
Technique: Electron Microscopy
Resolution: 3.47
Aggregation State: PARTICLE
Reconstruction method:

Abstract of the PDB Structure's related Publication:

Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps.

Download RCSB-PDB Structures:

Pdb Files   6RBD.pdb  
Pdbx/mmCIF Files   6RBD.cif   6ZQD.cif   6ZQE.cif   6ZQF.cif   6ZQG.cif   7AJU.cif  


Protein sequence:

MGKAAKKKYSGATSSKQVSAEKHLSSVFKFNTDLGQHILKNPLVAQGIVDKAQIRPSDVVLEVGPGTGNLTVRILEQAKNVVAVEMDPRMAAELTKRVRGTPVEKKLEIMLGDFMKTELPYFDICISNTPYQISSPLVFKLINQPRPPRVSILMFQREFALRLLARPGDSLYCRLSANVQMWANVTHIMKVGKNNFRPPPQVESSVVRLEIKNPRPQVDYNEWDGLLRIVFVRKNRTISAGFKSTTVMDILEKNYKTFLAMNNEMVDDTKGSMHDVVKEKIDTVLKETDLGDKRAGKCDQNDFLRLLYAFHQVGIHFS

Comments:

SceRsmA (formerly Dim1p) dimethylates two adjacent A (positions 1779 and 1780; 1518 and 1519 in E. coli numberings) in the loop of a conserved hairpin h45 near the 3′-end of 18S rRNA. AdoMet is the methyl group donor. RsmA can bind on naked rRNA but the target bases cannot be methylated before a subset of ribosomal proteins have bound. Dim2p could be a cofactor. Bacterial RsmA (KsgA) is the ortholog of yeast RsmA (Dim1p). They belong to the erm family of methyltransferases responsible for erythromycin resistance. RsmA homologs exists also Archaea. Notice, the acronym RsmA has also been used for for Regulator of Secondary Metabolism A, a protein not related to the RNA small subunit Methyltransferase.





Alpha Fold Predicted Structure:






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Protein sequence:

M G K A A K K K Y S G A T S S K Q V S A E K H L S S V F K F N T D L G Q H I L K N P L V A Q G I V D K A Q I R P S D V V L E V G P G T G N L T V R I L E Q A K N V V A V E M D P R M A A E L T K R V R G T P V E K K L E I M L G D F M K T E L P Y F D I C I S N T P Y Q I S S P L V F K L I N Q P R P P R V S I L M F Q R E F A L R L L A R P G D S L Y C R L S A N V Q M W A N V T H I M K V G K N N F R P P P Q V E S S V V R L E I K N P R P Q V D Y N E W D G L L R I V F V R K N R T I S A G F K S T T V M D I L E K N Y K T F L A M N N E M V D D T K G S M H D V V K E K I D T V L K E T D L G D K R A G K C D Q N D F L R L L Y A F H Q V G I H F S
50100150200250300SequenceGHTBSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P41819-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P41819-F1.cif  
DSSP Secondary Structures   P41819.dssp  





Publications: