EG10343

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Author Information

Angela Li (asli)

Basic Information

  • ID: EG10343
  • Name: rsmD (Ribosomal RNA small subunit methyltransferase D)
  • Organism: E. Coli
  • Description: This protein is a methyltransferase which methylates the G at position 966 of the 16S rRNA, a part of a hairpin loop [1]. The enzyme binds 16S ribosomal subunits with the unmethylated G966 rather than unmethylated rRNA directly. The methylation of G966 and the following nucleotide (G967) appear to stabilize the binding of an initiator tRNA to the 30S complex before it recognizes the start codon. Thus, it is considered to potentially regulate the early stages of translation initiation. [3] In fact, deletion of rsmD changes the frequency of certain translation initiation codons [4].
  • DNA Length: 597 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 198 amino acids.
  • Amino Acid sequence:

MKKPNHSGSGQIRIIGGQWRGRKLPVPDSPGLRPTTDRVRETLFNWLAPVIVDAQCLDCFAGSGALGLEALSRYAAGATLIEMDRAVSQQLIKNLATLKAGNARVVNSNAMSFLAQKGTPHNIVFVDPPFRRGLLEETINLLEDNGWLADEALIYVESEVENGLPTVPANWSLHREKVAGQVAYRLYQREAQGESDAD

Function and Homologs

  • Product: Ribosomal RNA small subunit methyltransferase D
  • Module: rRNA methylation (GO term)
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 16S rRNA (guanine(966)-N(2))-methyltransferase [Shigella sonnei], 407/100%/7e-144/99% WP_077124798.1
    • 16S rRNA (guanine(966)-N(2))-methyltransferase [Shigella boydii], 407/100%/7e-144/99%, wP_078166684.1
    • 16S rRNA (guanine(966)-N(2))-methyltransferase [Shigella dysenteriae], 406/100%/1e-143/99%, [1]
  • Equivalent E. coli / JCVI functional protein: MMSYN1 0202.

Expression

  • Expression Level: Medium
  • Expression Level Hypothesis: This gene is likely moderately expressed because it is not essential for ribosome biogenesis but rather plays a regulatory role by helping stabilize the binding of an initiator tRNA to the small ribosome subunit.
  • Expression Level References and Description: Medium expression levels from the E Coli proteomic dataset (75 copies / cell). Also the EcoCyc page for rsmD [here].
  • Expression Time: Early
  • Expression Time Hypothesis: Since it helps with the binding of the initiator tRNA to the small ribosome subunit, it must be expressed pretty early so that ribosomes can function optimally and all of the proteins can be properly translated. However, there is no evidence saying that it is essential to initiator tRNA binding (most likely its stabilization just facilitates the binding), so it does not have to be expressed right at the beginning.

Gene Context

  • Other Components: This module only has one component in the sense that the rsmD protein product is an functional enzyme itself (i.e. it doesn't need any other subunits) and because it directly methylates rRNA it isn't part of a metabolic pathway either. Enzymes that perform related functions of rRNA methylation are rsmH and rmsG.
  • Possible Dependencies: Era modifies rRNA precursors into 16S rRNA. Therefore, it helps produce the rRNA which rsmD methylates.
  • Process: rRNA methylation
    • Inputs: S-adenosyl-L-methionine, guanine at position 966 in 16S rRNA
    • Outputs: S-adenosyl-L-homocysteine, N2-methyl-guanine at position 966 in 16S rRNA
    • Resources: [EcoCyc]

Construct

  • 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