Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA small subunit methyltransferase H
Synonym: mraW
GI: 42560200
COG: COG0275
UniProt: P60390
Structures: | 3TKA |
Alpha Fold Predicted Structure: AF-P60390-F1
Enzyme type: methyltransferase
Position of modification - modification: s:1402(1402) - m4Cm


PDB Structures:


3TKA

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

RsmH is a specific AdoMet-dependent methyltransferase (MTase) responsible for N(4)-methylation of C1402 in 16S rRNA and conserved in almost all species of bacteria. The methylcytidine interacts with the P-site codon of the mRNA and increases ribosomal decoding fidelity. In this study, high resolution crystal structure (2.25Å) of Escherichia coli RsmH in complex with AdoMet and cytidine (the putative rRNA binding site) was determined. The structural analysis demonstrated that the complex consists of two distinct but structurally related domains: the typical MTase domain and the putative substrate recognition and binding domain. A deep pocket was found in the conserved AdoMet binding domain. It was also found that the cytidine bound far from AdoMet with the distance of 25.9Å. It indicates that the complex is not in a catalytically active state, and structural rearrangement of RsmH or the nucleotides neighboring C1402 may be necessary to trigger catalysis. Although there is only one molecule in the asymmetric unit of the crystals, RsmH can form a compact dimer across a crystallographic twofold axis. Further analysis of RsmH by small-angle X-ray scattering (SAXS) also revealed the dimer in solution, but with a more flexible conformation than that in crystal, likely resulting from the absence of the substrate. It implies that an active status of RsmH in vivo is achieved by a formation of the dimeric architecture. In general, crystal and solution structural analysis provides new information on the mechanism of the methylation of the fine-tuning ribosomal decoding center by the RsmH.

Download RCSB-PDB Structures:

Pdb Files   3TKA.pdb  
Pdbx/mmCIF Files   3TKA.cif  


Protein sequence:

MMENYKHTTVLLDEAVNGLNIRPDGIYIDGTFGRGGHSRLILSQLGEEGRLLAIDRDPQAIAVAKTIDDPRFSIIHGPFSALGEYVAERDLIGKIDGILLDLGVSSPQLDDAERGFSFMRDGPLDMRMDPTRGQSAAEWLQTAEEADIAWVLKTYGEERFAKRIARAIVERNREQPMTRTKELAEVVAAATPVKDKFKHPATRTFQAVRIWVNSELEEIEQALKSSLNVLAPGGRLSIISFHSLEDRIVKRFMRENSRGPQVPAGLPMTEEQLKKLGGRQLRALGKLMPGEEEVAENPRARSSVLRIAERTNA

Comments:

RsmH methylates N4 atom of C1402 (m4C) within a heavily hypermodified region of helix 44 in the 3’-terminal region of 16S rRNA. AdoMet is the methyl group donor. This enzyme is conserved in almost all species of bacteria. Together with 2’-O-methyltransferase RsmI, it allows the formation of the final product m4Cm. Phylogenetic profiling (co-occurrence) reavealed probable biochemical links between RsmH and translation factors IF2, RF1 and LepA.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Cm:m4Cm RNA rRNA 1402 SSU-16S Prokaryotic Cytosol 19965768   
C:m4C RNA rRNA 1402 SSU-16S Prokaryotic Cytosol 19965768   
m4C:m4,4C RNA rRNA 1402 SSU-16S Prokaryotic Cytosol
m4Cm:m4,4Cm RNA rRNA 1402 SSU-16S Prokaryotic Cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P60390-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P60390-F1.cif  
DSSP Secondary Structures   P60390.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Kimura S, Suzuki T Nucleic Acids Res [details] 19965768 -
RNA nucleotide methylation. Motorin Y, Helm M. Wiley Interdiscip Rev RNA [details] 21823225 -
Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA. Wei Y, Zhang H, Gao ZQ, Wang WJ, Shtykova EV, Xu JH, Liu QS, Dong YH... J Struct Biol [details] 22561317 -