Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase Nep1
Synonym: MJ0557
GI: 20532166
COG: COG1756
UniProt: Q57977
Structures: | 3BBE | 3BBD | 3BBH |
Alpha Fold Predicted Structure: AF-Q57977-F1
Enzyme type: methyltransferase
Position of modification - modification: s:914(966) - m1Y


PDB Structures:


3BBE

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 A resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.

Download RCSB-PDB Structures:

Pdb Files   3BBD.pdb   3BBE.pdb   3BBH.pdb  
Pdbx/mmCIF Files   3BBD.cif   3BBE.cif   3BBH.cif  


Protein sequence:

MTYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF

Comments:




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Y:m1Y RNA rRNA 914 SSU-16S Prokaryotic Cytosol 20047967   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M T Y N I I L A K S A L E L I P E E I K N K I R K S R V Y K Y D I L D S N Y H Y K A M E K L K D K E M R G R P D I I H I S L L N I L D S P I N H E K K L N I Y I H T Y D D K V L K I N P E T R L P R N Y F R F L G V M E K V L K G E R N H L I K M E E K T L E D L L N E I N A K K I A I M T K T G K L T H P K L L K E Y D T F I I G G F P Y G K L K I N K E K V F G D I K E I S I Y N K G L M A W T V C G I I C Y S L S 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-Q57977-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q57977-F1.cif  
DSSP Secondary Structures   Q57977.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Taylor AB, Meyer B, Leal BZ, Kotter P, Schirf V, Demeler B, Hart PJ, Entian KD, Wohnert J Nucleic Acids Res [details] 18208838 -
Backbone resonance assignments of the 48 kDa dimeric putative 18S rRNA-methyltransferase Nep1 from Methanocaldococcus jannaschii. Wurm JP, Duchardt E, Meyer B, Leal BZ, Kotter P, Entian KD, Wohnert J Biomol NMR Assign [details] 19779849 -
The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Wurm JP, Meyer B, Bahr U, Held M, Frolow O, Kotter P, Engels JW, Heckel A, Karas M, Entian KD, Wohnert J Nucleic Acids Res [details] 20047967 -