MMSYN1 0517

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Author Information

Michael Xie SUID: sxie

Basic Information

  • ID: MMSYN1_0517
  • Name: rluD
  • Organism: JCVI-syn3.0
  • Description: Responsible for synthesis of pseudouridine from uracil [1]. This is part of the S4 domain, which refers to a small RNA-binding protein domain found in a ribosomal protein named S4. Pseudouridine is commonly found in tRNA [2]. It may be involved in translation initiation and may also offer protection from radiation [3]. Disruption of rluD causes defects in ribosome assembly and causes a severe lack of growth [4].
  • DNA Length: 930 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 310 amino acids.
  • Amino Acid sequence:

MNKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFVVKPNSQITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLSNTNNTIVNALLASDVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKTHKLLSEMFKNHQIYKEYLAIVSGVIKPNKGLIDAPIGRSQIDRKKMSVTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQIRVHFNYINHPVLNDPVYGKKHQEFTDFGQYLHAYKLRFTHPITKKEIELISPLPKEFDDKIKELRGENND

Function and Homologs

  • Product: ribosomal large subunit pseudouridine synthase D
  • Module: pseudouridine synthase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • ribosomal large subunit pseudouridine synthase D [Mycoplasma mycoides], 624, 100%, 0.0, 100%, WP_020862809.1
    • pseudouridine synthase [Mycoplasma mycoides], 619, 100%, 0.0, 99%, WP_017697736.1
    • pseudouridine synthase [Mycoplasma mycoides], 616,, 100%, 0.0, 98%, WP_011166761.1
  • Equivalent E. coli / JCVI functional protein: EG12098

Expression

  • Expression Level: Low
    • Expression Level Hypothesis: A similar pseudouridine synthase for the large ribosomal subunit was classified into the low expression category, and since this is a similar gene, we expect the same level of expression; although we find this data in the context of E. coli, there is reason to believe that this particular gene is conserved and needed across the organisms at a similar rate due to the fundamental nature of the protein.
    • Expression Level References: The expression level data was gathered from analogy in the protein abundance profile study [5].
  • Expression Time: Early
    • Expression Time Hypothesis: This is an enzyme necessary for a functioning central dogma, as it has a role in ribosomal assembly.
    • Expression Time References: Research description above.

Gene Context

  • Other Components: No other components in the functional module.
  • Possible Dependencies: RNA polymerase, since rRNA (containing uridine) is needed for pseudouridine synthesis.
  • Process: Catalysis of pseudouridine synthesis
    • Inputs: 23S rRNA uridine1911/uridine1915/uridine1917
    • Outputs: 23S rRNA pseudouridine1911/pseudouridine1915/pseudouridine1917
    • Reference: Leppik, M.; Peil, L.; Kipper, K.; Liiv, A.; Remme, J. (2007). "Substrate specificity of the pseudouridine synthase RluD in Escherichia coli". FEBS J. 274: 5759–5766. doi:10.1111/j.1742-4658.2007.06101.x. PMID 17937767 (Taken from E.coli as this is highly conserved)

Construct

  • Predicted Translation Rate:
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • http://www.uniprot.org/uniprot/A0A014NNQ5
  • Hamma T, Ferré-D'Amaré AR (2006). "Pseudouridine synthases". Chem. Biol. 13 (11): 1125–1135. doi:10.1016/j.chembiol.2006.09.009. PMID 17113994.
  • Monobe, Manami; Arimoto-Kobayashi, Sakae; Ando, Koichi (2003). "β-Pseudouridine, a beer component, reduces radiation-induced chromosome aberrations in human lymphocytes". Mutation research. Genetic toxicology and environmental mutagenesis. 538 (1–2): 93–99. doi:10.1016/S1383-5718(03)00094-9. PMID 12834758.
  • GUTGSELL NS, DEUTSCHER MP, OFENGAND J. The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. RNA. 2005;11(7):1141-1152. doi:10.1261/rna.2550105.
  • Ishihama et al., Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics 20089:102 DOI: 10.1186/1471-2164-9-102
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