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Author Information

Eva Frankel

Basic Information

  • ID: EG11085
  • Name: rsmH
  • Organism: E. Coli
  • Description: Generally speaking, methyltransferases do precisely what their etomology implies: they transfer methyl. [1] This enzyme specifically catalyzes the reaction S-adenosyl-L-methionine + cytosine(1402) in 16S rRNA = S-adenosyl-L-homocysteine + N(4)-methylcytosine(1402) in 16S rRNA. [2] RsmH methylates cytidine at the N4 position. This function is important because the methylation of this nucleotide is involved in translation initiation at start codons that are non-AUG. [3]
  • DNA Length: 942
  • DNA sequence:


  • Amino Acid length: 319
  • Amino Acid sequence:


Function and Homologs

  • Product: Ribosomal RNA small subunit methyltransferase H
  • Module: rRNA base methylation
  • Closest homologous proteins:
    • MULTISPECIES: ribosomal RNA small subunit methyltransferase H [Proteobacteria], 634/100%/0.0/100% [4]
    • 16S rRNA (cytosine(1402)-N(4))-methyltransferase [Escherichia fergusonii], 633/100%/0.0/99%, [5]
    • ribosomal RNA small subunit methyltransferase H [Shigella sonnei], 632/100%/0.0/99%, [6]
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0524


  • Expression Level: Medium
  • Expression Level Hypothesis: rsmH has a highly specified catalytic activity. It is responsible for catalyzing one methylation reaction. This reaction is also not essential for function, although it may increase the efficiency of protein translation. Therefore, a high expression would be overkill. However, proper functioning of rRNA is extremely important for the gene to properly construct other proteins, so it must be expressed at a medium level.
  • Expression Level References and Description: I used the E. Coli database, where rsmH is expressed at 498 protein copies/cell (medium). More information also found here.
  • Expression Time: Early
  • Expression Level Hypothesis: Base methylation occurs late in ribosome maturation, but the rRNA itself should be expressed early so that it can synthesize proteins. This is crucial and must happen immediately in the cell.
  • Expression Time References and Description: Deduced from function & some details here

Gene Context

  • Other Components: EG10343
  • Possible Dependencies: EG10270 processes 16S rRNA. 16S rRNA is involved in both the inputs and the outputs of the process that this gene catalyzes; therefore, rsmH is dependent on this component for proper expression.
  • Process: S-adenosyl-L-methionine + a cytidine1402 in 16S rRNA → S-adenosyl-L-homocysteine + an N4-methylcytidine1402 in 16S rRNA + H+
    • Inputs: S-adenosyl-L-methionine, cytosine(1402) in 16S rRNA
    • Outputs: S-adenosyl-L-homocysteine, N(4)-methylcytosine(1402) in 16S rRNA


We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file