EG11782 dkm0713

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Author Information

Dana Murphy

Basic Information

  • ID: EG11782
  • Name: smpB
  • Organism: E. coli
  • Description: This gene is required to handle marking ribosomes for trans-translation [1], or the mediation of ribosomes that have been stalled during the translation process. [2] It binds to tmRNA RNA, which mimics the tRNA shape, and replaces the anticodon stem-loop in a gene with SmpB (tmRNA basically acts like tRNA during trans-translation). [3] Up to three SmpBs can bind to each tmRNA- one binds to the 3' end, the other two bind with the anticodon-like stem region [1]. smpB may also help protect tmRNA from degradation [3] and can act as a less efficient recipient in cell-to-cell plasmid transfers [1]. After the trans-translation occurs, the ribosome is freed to resume regular translation. SmpB is a member of the SsrA tagging complex [1].
  • DNA Length: 483 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 160 amino acids.
  • Amino Acid sequence:

MTKKKAHKPGSATIALNKRARHEYFIEEEFEAGLALQGWEVKSLRAGKANISDSYVLLRD GEAFLFGANITPMAVASTHVVCDPTRTRKLLLNQRELDSLYGRVNREGYTVVALSLYWKN AWCKVKIGVAKGKKQHDKRSDIKEREWQVDKARIMKNAHR

Function and Homologs

  • Product: SsrA-binding protein
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • MULTISPECIES: SsrA-binding protein [Proteobacteria], 332/100%/1e-115/100%, WP_000162574.1
    • SsrA-binding protein [Shigella sp. SF-2015], 332/100%/2e-115/99%, WP_000162572.1
    • SsrA-binding protein [Shigella sonnei], 331/100%/3e-115/99%, WP_052974463.1
  • Equivalent E. coli / JCVI functional protein: [MMSYN1_0776].

Expression

  • Expression Level: Medium
    • Expression Level Hypothesis: The gene is generally called upon when things go wrong, which should hopefully already limit its expression level. However, as many as three SmpBs are used to mediate each stalled ribosomes, which could explain why it has a medium expression level rather than a low one.
    • Expression Level References and Description: Data from the file EcoliProteomicExpressionData
  • Expression Time: Late
    • Expression Level Hypothesis: This gene's function is to fix things. It is only needed when other functions like translation have been running long enough to falter.
    • Expression Time References and Description: "analysis of affinity purified tmRNA·ribosome complexes also suggested the presence of only one SmpB molecule at a late stage of the trans-translation process" [source]


Gene Context

  • Other Components: tmRNA
  • Possible Dependencies: tRNA modification
  • Reactions: tmRNA + smpB(1-3) = tRNA [source]
    • Inputs: tmRNA, smpB
    • Outputs: tRNA

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file