MMSYN1 0202

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Author Information

Angela Li (asli)

Basic Information

  • ID: MMSYN1_0202
  • Name: rsmD
  • Organism: JCVI-Syn3.0
  • 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. [1]
  • DNA Length: 558 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 185 amino acids.
  • Amino Acid sequence:

MHIISGKYKKMKLQTLDSSITRPTLTRIKEDMFNIISNYFIFENKTSLDLFGGSGSLSIEGLSRGIKFAIINDLNKDANKIISFNLKKIPTSDYVLYQKDYLELLNLLKIQHQKVDLVYLDPPFKEIDYYYVVFDFLINNNLLNDWAIIISETNQKLDLTKIKDLNLLKFKDYNKKYLYIFRLEK

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.
    • Hypothetical protein, putative RNA methyltransferase, RsmD family [Mycoplasma mycoides subsp. capri PG3], 358/100/4e-125/98%, EXU60335.1
    • DNA methylase [Mycoplasma capricolum], 354/100/3e-123/97%, WP_011387095.1
    • DNA methylase [Mycoplasma leachii], 350/100/9e-122/96%, WP_013447561.1
  • Equivalent E. coli / JCVI functional protein: EG10343

Expression

  • Expression Level: Medium
  • Expression Level Hypothesis: I was unable to find rsmD in the Mycoplasma genitalium data, so I am not entirely sure, but because it is also a 16S rRNA methyltransferase like ksgA, I hypothesize that its methylation is ultimately a step in 16S rRNA processing. However, it may also play somewhat of a regulatory role because it binds the 16S subunit rather than just the rRNA itself. Furthermore, the homologous protein in E. Coli plays a regulatory role in translation initiation. Given these possible regulatory roles, it may not necessarily need to be expressed very highly (regulatory molecules are usually expressed at low or moderate amounts).
  • Expression Level References and Description: [Uniprot page on rsmD] and also the Uniprot page for the corresponding E. Coli gene [here].
  • Expression Time: Early
  • Expression Level Hypothesis: It's early because of its function within the context of the ribosome (i.e. 16S rRNA methylation), which is the protein production machinery for a cell. However, because there's no evidence that it is required for biogenesis of the ribosome, it probably doesn't need to be expressed right at the beginning, but should be expressed early for its possible regulatory roles.
  • Expression Time References and Description: [Uniprot page on rsmD] and also the Uniprot page for the corresponding E. Coli gene [here].

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 gidB
  • Possible Dependencies: Era modifies rRNA precursors into 16S rRNA. Therefore, it helps produce the rRNA which rsmD methylates.
  • Process: rRNA base methylation
    • Inputs: guanine at position 966
    • Outputs: methylated guanine at position 966
    • Resource: [Uniprot]

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