MMSYN1 0692 ri25chen

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Author Information

Ri Chen

Basic Information

  • ID: MMSYN1_0692
  • Name: pseudouridine synthase, RluA family
  • Organism: JCVI-Syn3.0
  • Description: Pseudouridine synthases are the enzymes responsible for the most abundant posttranscriptional modification of cellular RNAs. These enzymes catalyze the site-specific isomerization of uridine residues that are already part of an RNA chain, and appear to employ both sequence and structural information to achieve site specificity. Crystallographic analyses have demonstrated that all pseudouridine synthases share a common core fold and active site structure and that this core is modified by peripheral domains, accessory proteins, and guide RNAs to give rise to remarkable substrate versatility.[1]

Responsible for synthesis of pseudouridine from uracil-746 in 23S ribosomal RNA and from uracil-32 in the anticodon stem and loop of transfer RNAs. Catalytic activity: RNA uridine => RNA pseudouridine.[2] It is commonly found in tRNA, associated with thymidine and cytosine in the TΨC arm and is one of the invariant regions of tRNA. The function of it is not very clear, but it is expected to play a role in association with aminoacyl transferases during their interaction with tRNA, and hence in the initiation of translation. Recent studies suggest it may offer protection from radiation.[3] Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains.[4]

  • DNA Length: 906 base pairs.
  • DNA sequence (no stop codon):

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

  • Amino Acid length: 302 amino acids.
  • Amino Acid sequence:

MTKFVVNKNDQNQTLFKFLKKTFKTTPISVIYKWIRNKSIKINSKRISDKNYLLKINDVIEVYDSNKPIIRDQFNYISNVNLDIVYEDNNILIVNKPNNLEMHSTYNLCLDDMVKSYLVDKKEYDIYLENSFVISHVHRLDKLTSGLVIYAKNKISSTILTNAFKSKDQINKYYYALTSSDWSLDEFLQVNGYINYDSNIKKADFSLDKKNNYKYCQTEFKLINKNLILVKLITGKKHQIRSVLSFYNHPILNDFRYNGKKINDLKMIYLSAFKIEFKNLEKPLDYLNNKVFIKNPEWISKE

Function and Homologs

  • Functional Category: RNA
  • Product: 23S Pseudouridine synthase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • 23S rRNA pseudouridine synthase [Mycoplasma mycoides], 592/100%/0/100%, WP_020862916.1
    • pseudouridine synthase [Mycoplasma capricolum], 551/100%/0.0/92%, WP_036432238.1
    • RNA pseudouridine synthase [Mycoplasma leachii], 548/100%/0.0/92%, WP_013447985.1
  • Equivalent E. coli / JCVI functional protein: [EG12609].

[EcoCyc]

Expression

  • Expression Level: High (not on excel sheet)
  • Expression Level Hypothesis: Expression is high because pseudouridine synthases are the enzymes responsible for the most abundant posttranscriptional modification of cellular RNAs. These enzymes catalyze the site-specific isomerization of uridine residues that are already part of an RNA chain, and appear to employ both sequence and structural information to achieve site specificity. The function of it is not very clear, but it is expected to play a role in association with aminoacyl transferases during their interaction with tRNA, and hence in the initiation of translation. Recent studies suggest it may offer protection from radiation.
  • Expression Level References and Description: Not located on either M. genitalium model data nor the E. coli proteome. The expression level is induced due to the function of the gene.
  • Expression Time: At which time should the gene be expressed in the lifecycle of our organism? Right at beginning
  • Expression Level Hypothesis: RNA is a critical component of producing new proteins: we need to produce more functioning RNA in order to synthesize later components, and it seems that pseudouridine synthases are the enzymes responsible for the most abundant posttranscriptional modification of cellular RNAs.
  • Expression Time References and Description: 1234

Gene Context

  • Other Components: none
  • Possible Dependencies: tRNA ligase The enzyme interacts with tRNA to play a role in association with aminoacyl transferases
  • Process: post-transcriptional modification of cellular RNAs
    • Inputs: Uridine, Ψ synthase
    • Outputs: Pseudouridine synthase (not much information, unclear)
    • Reference: [1]

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
  • [2], PubMed
  • [3], UniProt
  • [4], Refdoc
  • [5], InterPro
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