EG12098

From BioE80 Boot
Jump to: navigation, search

Author Information

Michael Xie SUNET ID: sxie

Basic Information

  • ID: EG12098
  • Name: rluD
  • Organism: E. coli
  • Description: RluD is a pseudouridine synthase that catalyzes pseudouridine formation at positions 1911, 1915, and 1917 in helix 69 (H69) of the 23S rRNA.

Experiments using an rluD deletion strain showed that the loss of pseudouridylation at positions 1911, 1915, and 1917 in 23S rRNA leads to a defect in ribosome assembly, biogenesis and function [1]. Pseudouridine bases may also have function in initiation and termination of translation [2].

  • DNA Length: 978 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 326 amino acids.
  • Amino Acid sequence:

MAQRVQLTATVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVL GGEQVAINAEIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALL HYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMT AGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHM AHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAP IPQDMVELIEVMRADFEEHKDEVDWL

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.
    • MULTISPECIES: ribosomal large subunit pseudouridine synthase D [Proteobacteria] 666 100% 0.0 100% WP_000079100.1
    • ribosomal large subunit pseudouridine synthase D [Escherichia coli] 665 100% 0.0 99% WP_021547682.1
    • MULTISPECIES: ribosomal large subunit pseudouridine synthase D [Enterobacteriaceae] 665 100% 0.0 99% WP_000079112.1
  • Equivalent E. coli / JCVI functional protein: MMSYN1_0517

Expression

  • Expression Level: Low
    • Expression Level Hypothesis: Pseudouridine synthase D for the large ribosomal subunit was classified into the low expression category in the Ishihama study.
    • Expression Level References: The expression level data was gathered from analogy in the protein abundance profile study [3].
  • Expression Time: Early
    • Expression Time Hypothesis: This is one of the enzymes 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 RNA (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

Construct

  • Predicted Translation Rate:
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file
  • 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.
  • https://ecocyc.org/gene?orgid=ECOLI&id=EG12098
  • Ishihama et al., Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics 20089:102 DOI: 10.1186/1471-2164-9-102
  • Retrieved from "http://e80boot.org/index.php?title=EG12098&oldid=7824"