EG11085

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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:

ATG ATG GAG AAT TAC AAG CAT ACG ACG GTG TTA TTA GAT GAG GCA GTC AAT GGG TTA AAC ATT CGT CCG GAC GGG ATC TAT ATC GAC GGA ACA TTC GGACGT GGA GGA CAC TCT CGC CTG ATT TTG TCC CAG CTG GGT GAA GAG GGG CGT TTA TTA GCT ATC GAT CGC GAT CCG CAA GCG ATC GCC GTA GCA AAA ACTATC GAC GAC CCC CGT TTC TCA ATT ATT CAC GGA CCG TTT TCA GCG CTG GGC GAG TAT GTC GCT GAG CGC GAC TTA ATC GGC AAA ATT GAC GGG ATT CTTTTG GAC CTT GGC GTA TCT TCA CCC CAA TTG GAC GAT GCC GAG CGC GGG TTC TCG TTC ATG CGT GAC GGA CCT TTA GAC ATG CGT ATG GAC CCG ACA CGCGGT CAA AGT GCC GCG GAA TGG CTT CAA ACG GCC GAG GAA GCG GAC ATC GCC TGG GTC CTT AAG ACC TAC GGC GAA GAG CGC TTC GCA AAG CGT ATC GCACGC GCT ATC GTC GAG CGT AAC CGT GAG CAG CCT ATG ACT CGC ACT AAA GAG CTG GCG GAA GTG GTC GCC GCT GCA ACC CCT GTA AAA GAT AAA TTT AAGCAT CCG GCG ACA CGC ACT TTT CAA GCG GTT CGT ATT TGG GTA AAC TCT GAG TTG GAG GAG ATT GAA CAA GCA CTT AAA TCA TCG CTG AAC GTT CTG GCTCCA GGT GGC CGT CTG AGT ATT ATT TCT TTC CAT TCG TTG GAG GAT CGC ATT GTA AAA CGC TTC ATG CGT GAG AAC AGC CGC GGT CCA CAG GTA CCG GCTGGT CTG CCT ATG ACC GAA GAA CAG TTG AAA AAG TTA GGT GGT CGC CAG TTA CGC GCC CTT GGA AAA CTG ATG CCA GGT GAA GAA GAA GTT GCC GAG AACCCT CGC GCA CGT TCC TCC GTT TTA CGC ATT GCG GAA CGC ACA AAT GCG TAA

  • Amino Acid length: 319
  • Amino Acid sequence:

MMENYKHTTVLLDEAVNGLNIRPDGIYIDGTFGRGGHSRLILSQLGEEGRLLAIDRDPQA IAVAKTIDDPRFSIIHGPFSALGEYVAERDLIGKIDGILLDLGVSSPQLDDAERGFSFMR DGPLDMRMDPTRGQSAAEWLQTAEEADIAWVLKTYGEERFAKRIARAIVERNREQPMTRT KELAEVVAAATPVKDKFKHPATRTFQAVRIWVNSELEEIEQALKSSLNVLAPGGRLSIIS FHSLEDRIVKRFMRENSRGPQVPAGLPMTEEQLKKLGGRQLRALGKLMPGEEEVAENPRA RSSVLRIAERTNA

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

  • 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

Construct

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