Modomics - A Database of RNA Modifications

ID Card:

Full name: 18S rRNA (guanine-N(7))-methyltransferase
Synonym: MERM1, BUD23
GI: 21552765
UniProt: O43709
Structures: | 6G4W |
Alpha Fold Predicted Structure: AF-O43709-F1
Complex: WBSCR22-TRMT112
Enzyme type: methyltransferase
Position of modification - modification: s:1639(1338) - m7G


PDB Structures:


6G4W

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.

Download RCSB-PDB Structures:

Pdb Files   6G4W.pdb  
Pdbx/mmCIF Files   6G4W.cif  


Protein sequence:

MASRGRRPEHGGPPELFYDETEARKYVRNSRMIDIQTRMAGRALELLYLPENKPCYLLDIGCGTGLSGSYLSDEGHYWVGLDISPAMLDEAVDREIEGDLLLGDMGQGIPFKPGTFDGCISISAVQWLCNANKKSENPAKRLYCFFASLFSVLVRGSRAVLQLYPENSEQLELITTQATKAGFSGGMVVDYPNSAKAKKFYLCLFSGPSTFIPEGLSENQDEVEPRESVFTNERFPLRMSRRGMVRKSRAWVLEKKERHRRQGREVRPDTQYTGRKRKPRF

Comments:

WBSCR22 is required for N7 methylation at nucleotide G1639 of 18S rRNA. WBSCR22 interacts directly with TRMT112, forming a heterodimer, and that the latter protein is required for the metabolic stability of the former. Enzyme is required for distinct pre-rRNA processing reactions leading to synthesis of 18S rRNA, and it has been demonstrated that in human cells, as in budding yeast, ribosome biogenesis requires the presence of the modification enzyme rather than its RNA-modifying catalytic activity (Zorbas et al. 2015 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m7G RNA rRNA 1639 small rRNA subunit 18S Nucleolus 25851604   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-O43709-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O43709-F1.cif  
DSSP Secondary Structures   O43709.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis. Zorbas C, Nicolas E, Wacheul L, Huvelle E, Heurgué-Hamard V, Lafontaine DL. Mol Biol Cell [details] 25851604 10.1091/mbc.E15-02-0073