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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)DescriptionActionsGraphical viewLength
    Binding sitei43SubstrateUniRule annotation1 Publication1
    Active sitei48NucleophileUniRule annotation1 Publication1
    Binding sitei76SubstrateUniRule annotation1 Publication1
    Binding sitei179SubstrateUniRule annotation1 Publication1
    Binding sitei202SubstrateUniRule annotation1 Publication1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi19K → M or R: Reduced structural stability and decrease in activity. 1 Publication1
    Mutagenesisi20P → G or L: Reduced structural stability and no change in activity. 1 Publication1
    Mutagenesisi43H → A: 330-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → F: 2-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → G: 250-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → N: 180-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi43H → Q: 50-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi48D → C: Loss of activity. 1 Publication1
    Mutagenesisi58C → A: Slight increase in activity. Slight increase in activity; when associated with A-174 and A-193. 1 Publication1
    Mutagenesisi174C → A: Slight increase in activity. Slight increase in activity; when associated with A-58 and A-193. 1 Publication1
    Mutagenesisi193C → A: Slight increase in activity; when associated with A-58 and A-174. 1 Publication1
    Mutagenesisi193C → V: Slight increase in activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001218301 – 314tRNA pseudouridine synthase BAdd BLAST314

    Proteomic databases

    PaxDbiP60340.
    PRIDEiP60340.

    Interactioni

    Protein-protein interaction databases

    IntActiP60340. 5 interactors.
    STRINGi511145.b3166.

    Structurei

    Secondary structure

    1314
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi13 – 19Combined sources7
    Helixi25 – 35Combined sources11
    Beta strandi41 – 45Combined sources5
    Beta strandi52 – 59Combined sources8
    Helixi60 – 66Combined sources7
    Helixi67 – 70Combined sources4
    Beta strandi74 – 82Combined sources9
    Beta strandi84 – 90Combined sources7
    Beta strandi95 – 98Combined sources4
    Helixi105 – 113Combined sources9
    Beta strandi116 – 121Combined sources6
    Beta strandi125 – 127Combined sources3
    Helixi136 – 141Combined sources6
    Beta strandi151 – 164Combined sources14
    Beta strandi167 – 174Combined sources8
    Helixi180 – 190Combined sources11
    Beta strandi195 – 205Combined sources11
    Helixi210 – 212Combined sources3
    Helixi216 – 228Combined sources13
    Helixi234 – 237Combined sources4
    Helixi238 – 240Combined sources3
    Helixi246 – 248Combined sources3
    Beta strandi253 – 256Combined sources4
    Helixi258 – 264Combined sources7
    Turni265 – 267Combined sources3
    Beta strandi277 – 285Combined sources9
    Turni286 – 289Combined sources4
    Beta strandi290 – 297Combined sources8
    Beta strandi303 – 308Combined sources6

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP60340.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni124 – 152RNA bindingBy similarityAdd BLAST29

    Sequence similaritiesi

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

    Phylogenomic databases

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

    Family and domain databases

    Gene3Di2.30.130.10. 1 hit.
    HAMAPiMF_01080. TruB_bact. 1 hit.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1K8WX-ray1.85A7-314[»]
    1R3FX-ray1.85A1-314[»]
    1ZL3X-ray2.80A10-314[»]
    ProteinModelPortaliP60340.
    SMRiP60340.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP60340. 5 interactors.
    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.
    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. 1 hit.
    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...

    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: November 2, 2016
    This is version 115 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.