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Protein

tRNA pseudouridine synthase B

Gene

truB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.UniRule annotation2 Publications

Catalytic activityi

tRNA uridine(55) = tRNA pseudouridine(55).UniRule annotation1 Publication

Kineticsi

  1. KM=148 nM for tRNA (at pH 7.5)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei43 – 431SubstrateUniRule annotation1 Publication
    Active sitei48 – 481NucleophileUniRule annotation1 Publication
    Binding sitei76 – 761SubstrateUniRule annotation1 Publication
    Binding sitei179 – 1791SubstrateUniRule annotation1 Publication
    Binding sitei202 – 2021SubstrateUniRule annotation1 Publication

    GO - Molecular functioni

    • pseudouridine synthase activity Source: EcoCyc
    • RNA binding Source: InterPro

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    tRNA processing

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11177-MONOMER.
    ECOL316407:JW3135-MONOMER.
    MetaCyc:EG11177-MONOMER.
    BRENDAi5.4.99.25. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA pseudouridine synthase BUniRule annotation (EC:5.4.99.25UniRule annotation1 Publication)
    Alternative name(s):
    Protein p35
    tRNA pseudouridine(55) synthaseUniRule annotation
    Short name:
    Psi55 synthaseUniRule annotation
    tRNA pseudouridylate synthaseUniRule annotation
    tRNA-uridine isomeraseUniRule annotation
    Gene namesi
    Name:truB
    Synonyms:yhbA
    Ordered Locus Names:b3166, JW3135
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11177. truB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi19 – 191K → M or R: Reduced structural stability and decrease in activity. 1 Publication
    Mutagenesisi20 – 201P → G or L: Reduced structural stability and no change in activity. 1 Publication
    Mutagenesisi43 – 431H → A: 330-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi43 – 431H → F: 2-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi43 – 431H → G: 250-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi43 – 431H → N: 180-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi43 – 431H → Q: 50-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi48 – 481D → C: Loss of activity. 1 Publication
    Mutagenesisi58 – 581C → A: Slight increase in activity. Slight increase in activity; when associated with A-174 and A-193. 1 Publication
    Mutagenesisi174 – 1741C → A: Slight increase in activity. Slight increase in activity; when associated with A-58 and A-193. 1 Publication
    Mutagenesisi193 – 1931C → A: Slight increase in activity; when associated with A-58 and A-174. 1 Publication
    Mutagenesisi193 – 1931C → V: Slight increase in activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314tRNA pseudouridine synthase BPRO_0000121830Add
    BLAST

    Proteomic databases

    PaxDbiP60340.
    PRIDEiP60340.

    Interactioni

    Protein-protein interaction databases

    IntActiP60340. 5 interactions.
    STRINGi511145.b3166.

    Structurei

    Secondary structure

    1
    314
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi13 – 197Combined sources
    Helixi25 – 3511Combined sources
    Beta strandi41 – 455Combined sources
    Beta strandi52 – 598Combined sources
    Helixi60 – 667Combined sources
    Helixi67 – 704Combined sources
    Beta strandi74 – 829Combined sources
    Beta strandi84 – 907Combined sources
    Beta strandi95 – 984Combined sources
    Helixi105 – 1139Combined sources
    Beta strandi116 – 1216Combined sources
    Beta strandi125 – 1273Combined sources
    Helixi136 – 1416Combined sources
    Beta strandi151 – 16414Combined sources
    Beta strandi167 – 1748Combined sources
    Helixi180 – 19011Combined sources
    Beta strandi195 – 20511Combined sources
    Helixi210 – 2123Combined sources
    Helixi216 – 22813Combined sources
    Helixi234 – 2374Combined sources
    Helixi238 – 2403Combined sources
    Helixi246 – 2483Combined sources
    Beta strandi253 – 2564Combined sources
    Helixi258 – 2647Combined sources
    Turni265 – 2673Combined sources
    Beta strandi277 – 2859Combined sources
    Turni286 – 2894Combined sources
    Beta strandi290 – 2978Combined sources
    Beta strandi303 – 3086Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K8WX-ray1.85A7-314[»]
    1R3FX-ray1.85A1-314[»]
    1ZL3X-ray2.80A10-314[»]
    ProteinModelPortaliP60340.
    SMRiP60340. Positions 10-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP60340.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni124 – 15229RNA bindingBy similarityAdd
    BLAST

    Sequence similaritiesi

    Belongs to the pseudouridine synthase TruB family. Type 1 subfamily.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4105D0T. Bacteria.
    COG0130. LUCA.
    HOGENOMiHOG000231223.
    InParanoidiP60340.
    KOiK03177.
    OMAiYELQFIR.
    OrthoDBiEOG6358D3.
    PhylomeDBiP60340.

    Family and domain databases

    Gene3Di2.30.130.10. 1 hit.
    HAMAPiMF_01080. TruB_bact.
    InterProiIPR020103. PsdUridine_synth_cat_dom.
    IPR002501. PsdUridine_synth_N.
    IPR015947. PUA-like_domain.
    IPR014780. tRNA_psdUridine_synth_TruB.
    IPR015240. tRNA_sdUridine_synth_fam1_C.
    IPR032819. TruB_C.
    [Graphical view]
    PANTHERiPTHR13767. PTHR13767. 1 hit.
    PfamiPF09157. TruB-C_2. 1 hit.
    PF16198. TruB_C_2. 1 hit.
    PF01509. TruB_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF55120. SSF55120. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsiTIGR00431. TruB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P60340-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSRPRRRGRD INGVLLLDKP QGMSSNDALQ KVKRIYNANR AGHTGALDPL
    60 70 80 90 100
    ATGMLPICLG EATKFSQYLL DSDKRYRVIA RLGQRTDTSD ADGQIVEERP
    110 120 130 140 150
    VTFSAEQLAA ALDTFRGDIE QIPSMYSALK YQGKKLYEYA RQGIEVPREA
    160 170 180 190 200
    RPITVYELLF IRHEGNELEL EIHCSKGTYI RTIIDDLGEK LGCGAHVIYL
    210 220 230 240 250
    RRLAVSKYPV ERMVTLEHLR ELVEQAEQQD IPAAELLDPL LMPMDSPASD
    260 270 280 290 300
    YPVVNLPLTS SVYFKNGNPV RTSGAPLEGL VRVTEGENGK FIGMGEIDDE
    310
    GRVAPRRLVV EYPA
    Length:314
    Mass (Da):35,087
    Last modified:February 16, 2004 - v1
    Checksum:iFEA46C01E0E8E7A5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X13270 Genomic DNA. Translation: CAA31635.1.
    X13775 Genomic DNA. Translation: CAA32021.1.
    U18997 Genomic DNA. Translation: AAA57969.1.
    U00096 Genomic DNA. Translation: AAC76200.1.
    AP009048 Genomic DNA. Translation: BAE77212.1.
    S79856 Genomic DNA. Translation: AAB35645.1.
    PIRiS01916. Q9EC35.
    RefSeqiNP_417635.1. NC_000913.3.
    WP_000089698.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76200; AAC76200; b3166.
    BAE77212; BAE77212; BAE77212.
    GeneIDi947687.
    KEGGiecj:JW3135.
    eco:b3166.
    PATRICi32121750. VBIEscCol129921_3261.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X13270 Genomic DNA. Translation: CAA31635.1.
    X13775 Genomic DNA. Translation: CAA32021.1.
    U18997 Genomic DNA. Translation: AAA57969.1.
    U00096 Genomic DNA. Translation: AAC76200.1.
    AP009048 Genomic DNA. Translation: BAE77212.1.
    S79856 Genomic DNA. Translation: AAB35645.1.
    PIRiS01916. Q9EC35.
    RefSeqiNP_417635.1. NC_000913.3.
    WP_000089698.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K8WX-ray1.85A7-314[»]
    1R3FX-ray1.85A1-314[»]
    1ZL3X-ray2.80A10-314[»]
    ProteinModelPortaliP60340.
    SMRiP60340. Positions 10-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP60340. 5 interactions.
    STRINGi511145.b3166.

    Proteomic databases

    PaxDbiP60340.
    PRIDEiP60340.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76200; AAC76200; b3166.
    BAE77212; BAE77212; BAE77212.
    GeneIDi947687.
    KEGGiecj:JW3135.
    eco:b3166.
    PATRICi32121750. VBIEscCol129921_3261.

    Organism-specific databases

    EchoBASEiEB1164.
    EcoGeneiEG11177. truB.

    Phylogenomic databases

    eggNOGiENOG4105D0T. Bacteria.
    COG0130. LUCA.
    HOGENOMiHOG000231223.
    InParanoidiP60340.
    KOiK03177.
    OMAiYELQFIR.
    OrthoDBiEOG6358D3.
    PhylomeDBiP60340.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11177-MONOMER.
    ECOL316407:JW3135-MONOMER.
    MetaCyc:EG11177-MONOMER.
    BRENDAi5.4.99.25. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP60340.
    PROiP60340.

    Family and domain databases

    Gene3Di2.30.130.10. 1 hit.
    HAMAPiMF_01080. TruB_bact.
    InterProiIPR020103. PsdUridine_synth_cat_dom.
    IPR002501. PsdUridine_synth_N.
    IPR015947. PUA-like_domain.
    IPR014780. tRNA_psdUridine_synth_TruB.
    IPR015240. tRNA_sdUridine_synth_fam1_C.
    IPR032819. TruB_C.
    [Graphical view]
    PANTHERiPTHR13767. PTHR13767. 1 hit.
    PfamiPF09157. TruB-C_2. 1 hit.
    PF16198. TruB_C_2. 1 hit.
    PF01509. TruB_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF55120. SSF55120. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsiTIGR00431. TruB. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The existence of two genes between infB and rpsO in the Escherichia coli genome: DNA sequencing and S1 nuclease mapping."
      Sands J.F., Regnier P., Cummings H.S., Grunberg-Manago M., Hershey J.W.B.
      Nucleic Acids Res. 16:10803-10816(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli."
      Nurse K., Wrzesisnski J., Bakin A., Lane B.G., Ofengand J.
      RNA 1:102-112(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20, PROTEIN SEQUENCE OF 6-20, FUNCTION, CATALYTIC ACTIVITY, CHARACTERIZATION.
    5. "Role of cysteine residues in pseudouridine synthases of different families."
      Ramamurthy V., Swann S.L., Spedaliere C.J., Mueller E.G.
      Biochemistry 38:13106-13111(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF CYS-58; CYS-174 AND CYS-193.
      Strain: BLR-DE3 and K12 / JM109 / ATCC 53323.
    6. "Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues."
      Spedaliere C.J., Hamilton C.S., Mueller E.G.
      Biochemistry 39:9459-9465(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF LYS-19 AND PRO-20.
      Strain: BLR-DE3.
    7. "Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells."
      Gutgsell N., Englund N., Niu L., Kaya Y., Lane B.G., Ofengand J.
      RNA 6:1870-1881(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF ASP-48.
      Strain: BLR-DE3 and K12 / MG1655 / ATCC 47076.
    8. "The roles of the essential Asp-48 and highly conserved His-43 elucidated by the pH dependence of the pseudouridine synthase TruB."
      Hamilton C.S., Spedaliere C.J., Ginter J.M., Johnston M.V., Mueller E.G.
      Arch. Biochem. Biophys. 433:322-334(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF HIS-43.
    9. "Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme."
      Hoang C., Ferre-D'Amare A.R.
      Cell 107:929-939(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 10-314 IN COMPLEX WITH RNA, ACTIVE SITE.
    10. "Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit."
      Pan H., Agarwalla S., Moustakas D.T., Finer-Moore J., Stroud R.M.
      Proc. Natl. Acad. Sci. U.S.A. 100:12648-12653(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 1-314.

    Entry informationi

    Entry nameiTRUB_ECOLI
    AccessioniPrimary (citable) accession number: P60340
    Secondary accession number(s): P09171, P76671, Q2M944
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 16, 2004
    Last sequence update: February 16, 2004
    Last modified: January 20, 2016
    This is version 112 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.