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Protein

Pseudouridine-5'-phosphate glycosidase

Gene

psuG

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

Functioni

Catalyzes the reversible cleavage of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. Functions biologically in the cleavage direction, as part of a pseudouridine degradation pathway.UniRule annotation2 Publications

Catalytic activityi

Uracil + D-ribose 5-phosphate = pseudouridine 5'-phosphate + H2O.UniRule annotation2 Publications

Cofactori

Mn2+UniRule annotation2 Publications, Fe2+2 Publications, Co2+2 PublicationsNote: Binds 1 manganese ion per subunit. Can also use Fe2+ and Co2+. The unusual metal binding site is heavily hydrated, coordinated with an aspartate side chain and five water molecules, and likely plays a role in anchoring the PsiMP phosphate.2 Publications

Enzyme regulationi

Inhibited by Zn2+ and Ni2+.1 Publication

Kineticsi

kcat is 3.74 sec(-1) for the synthesis of PsiMP.1 Publication

  1. KM=60 µM for pseudouridine 5'-phosphate (in the presence of 0.5 mM Mn2+)1 Publication
  2. KM=169.6 µM for uracil1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei31 – 311Proton donor1 PublicationUniRule annotation
    Binding sitei93 – 931SubstrateUniRule annotation1 Publication
    Binding sitei113 – 1131Substrate; via amide nitrogenUniRule annotation1 Publication
    Metal bindingi145 – 1451ManganeseUniRule annotation1 Publication
    Active sitei166 – 1661Nucleophile1 PublicationUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase, Lyase

    Keywords - Ligandi

    Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12033-MONOMER.
    ECOL316407:JW2152-MONOMER.
    BRENDAi4.2.1.70. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pseudouridine-5'-phosphate glycosidase1 PublicationUniRule annotation (EC:4.2.1.70UniRule annotation2 Publications)
    Short name:
    PsiMP glycosidase1 PublicationUniRule annotation
    Gene namesi
    Name:psuGUniRule annotationImported
    Synonyms:pscG, yeiN1 Publication
    Ordered Locus Names:b2165, JW2152
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12033. psuG.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi31 – 311E → A: 7500-fold decrease in reaction rate while little change in substrate affinity. 1 Publication
    Mutagenesisi93 – 931K → A: 17-fold decrease in reaction rate while modest decrease in substrate affinity. 1 Publication
    Mutagenesisi149 – 1491D → A: Loss of activity. 1 Publication
    Mutagenesisi166 – 1661K → A: 2900-fold decrease in reaction rate while no change in substrate affinity. 1 Publication
    Mutagenesisi289 – 2891N → A: 17-fold decrease in reaction rate while modest decrease in substrate affinity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 312312Pseudouridine-5'-phosphate glycosidasePRO_0000169150Add
    BLAST

    Proteomic databases

    PaxDbiP33025.

    Interactioni

    Subunit structurei

    Homotrimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi4261702. 6 interactions.
    DIPiDIP-11926N.
    IntActiP33025. 13 interactions.
    MINTiMINT-1308217.
    STRINGi511145.b2165.

    Structurei

    Secondary structure

    1
    312
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni8 – 103Combined sources
    Beta strandi11 – 133Combined sources
    Helixi15 – 228Combined sources
    Beta strandi27 – 304Combined sources
    Helixi33 – 364Combined sources
    Helixi43 – 5715Combined sources
    Beta strandi61 – 688Combined sources
    Beta strandi71 – 755Combined sources
    Helixi78 – 8710Combined sources
    Helixi88 – 903Combined sources
    Beta strandi91 – 944Combined sources
    Turni96 – 983Combined sources
    Helixi99 – 1046Combined sources
    Beta strandi109 – 1113Combined sources
    Helixi113 – 12210Combined sources
    Beta strandi127 – 1293Combined sources
    Helixi140 – 1434Combined sources
    Helixi148 – 1558Combined sources
    Beta strandi159 – 1624Combined sources
    Helixi171 – 18010Combined sources
    Beta strandi185 – 1895Combined sources
    Beta strandi202 – 2043Combined sources
    Beta strandi206 – 2094Combined sources
    Helixi212 – 22413Combined sources
    Beta strandi231 – 2344Combined sources
    Helixi239 – 2413Combined sources
    Helixi245 – 26218Combined sources
    Helixi266 – 2683Combined sources
    Helixi269 – 28012Combined sources
    Turni281 – 2833Combined sources
    Helixi284 – 31027Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GIJX-ray1.94A/B/C1-312[»]
    4GIKX-ray2.19A/B/C1-312[»]
    4GILX-ray2.54A/B/C1-312[»]
    4GIMX-ray1.80A/B/C1-312[»]
    ProteinModelPortaliP33025.
    SMRiP33025. Positions 6-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni147 – 1493Substrate bindingUniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the pseudouridine-5'-phosphate glycosidase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105D53. Bacteria.
    COG2313. LUCA.
    HOGENOMiHOG000064311.
    InParanoidiP33025.
    KOiK16329.
    OMAiIIAHGMP.
    OrthoDBiEOG6B09RX.
    PhylomeDBiP33025.

    Family and domain databases

    HAMAPiMF_01876. PsiMP_glycosidase.
    InterProiIPR007342. PsuG.
    [Graphical view]
    PANTHERiPTHR10584:SF1. PTHR10584:SF1. 1 hit.
    PfamiPF04227. Indigoidine_A. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P33025-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSELKISPEL LQISPEVQDA LKNKKPVVAL ESTIISHGMP FPQNAQTAIE
    60 70 80 90 100
    VEETIRKQGA VPATIAIIGG VMKVGLSKEE IELLGREGHN VTKVSRRDLP
    110 120 130 140 150
    FVVAAGKNGA TTVASTMIIA ALAGIKVFAT GGIGGVHRGA EHTFDISADL
    160 170 180 190 200
    QELANTNVTV VCAGAKSILD LGLTTEYLET FGVPLIGYQT KALPAFFCRT
    210 220 230 240 250
    SPFDVSIRLD SASEIARAMV VKWQSGLNGG LVVANPIPEQ FAMPEHTINA
    260 270 280 290 300
    AIDQAVAEAE AQGVIGKEST PFLLARVAEL TGGDSLKSNI QLVFNNAILA
    310
    SEIAKEYQRL AG
    Length:312
    Mass (Da):32,910
    Last modified:February 1, 1994 - v1
    Checksum:iEBD892C271404F1F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00007 Genomic DNA. Translation: AAA60517.1.
    U00096 Genomic DNA. Translation: AAC75226.1.
    AP009048 Genomic DNA. Translation: BAE76642.1.
    PIRiD64985.
    RefSeqiNP_416670.1. NC_000913.3.
    WP_001292460.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75226; AAC75226; b2165.
    BAE76642; BAE76642; BAE76642.
    GeneIDi946699.
    KEGGiecj:JW2152.
    eco:b2165.
    PATRICi32119679. VBIEscCol129921_2250.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00007 Genomic DNA. Translation: AAA60517.1.
    U00096 Genomic DNA. Translation: AAC75226.1.
    AP009048 Genomic DNA. Translation: BAE76642.1.
    PIRiD64985.
    RefSeqiNP_416670.1. NC_000913.3.
    WP_001292460.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GIJX-ray1.94A/B/C1-312[»]
    4GIKX-ray2.19A/B/C1-312[»]
    4GILX-ray2.54A/B/C1-312[»]
    4GIMX-ray1.80A/B/C1-312[»]
    ProteinModelPortaliP33025.
    SMRiP33025. Positions 6-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261702. 6 interactions.
    DIPiDIP-11926N.
    IntActiP33025. 13 interactions.
    MINTiMINT-1308217.
    STRINGi511145.b2165.

    Proteomic databases

    PaxDbiP33025.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75226; AAC75226; b2165.
    BAE76642; BAE76642; BAE76642.
    GeneIDi946699.
    KEGGiecj:JW2152.
    eco:b2165.
    PATRICi32119679. VBIEscCol129921_2250.

    Organism-specific databases

    EchoBASEiEB1968.
    EcoGeneiEG12033. psuG.

    Phylogenomic databases

    eggNOGiENOG4105D53. Bacteria.
    COG2313. LUCA.
    HOGENOMiHOG000064311.
    InParanoidiP33025.
    KOiK16329.
    OMAiIIAHGMP.
    OrthoDBiEOG6B09RX.
    PhylomeDBiP33025.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12033-MONOMER.
    ECOL316407:JW2152-MONOMER.
    BRENDAi4.2.1.70. 2026.

    Miscellaneous databases

    PROiP33025.

    Family and domain databases

    HAMAPiMF_01876. PsiMP_glycosidase.
    InterProiIPR007342. PsuG.
    [Graphical view]
    PANTHERiPTHR10584:SF1. PTHR10584:SF1. 1 hit.
    PfamiPF04227. Indigoidine_A. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Automated multiplex sequencing of the E.coli genome."
      Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
      Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / BHB2600.
    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. "Molecular identification of pseudouridine-metabolizing enzymes."
      Preumont A., Snoussi K., Stroobant V., Collet J.-F., Van Schaftingen E.
      J. Biol. Chem. 283:25238-25246(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: K12.
    5. "Pseudouridine monophosphate glycosidase: a new glycosidase mechanism."
      Huang S., Mahanta N., Begley T.P., Ealick S.E.
      Biochemistry 51:9245-9255(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF APOENYZME AND COMPLEX WITH D-RIBITOL 5-PHOSPHATE AND WILD-TYPE AND MUTANT ALA-166 IN COMPLEX WITH PSEUDOURIDINE-5'-PHOSPHATE AND MANGANESE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVE SITE, REACTION MECHANISM, MUTAGENESIS OF GLU-31; LYS-93; ASP-149; LYS-166 AND ASN-289.
      Strain: K12.

    Entry informationi

    Entry nameiPSUG_ECOLI
    AccessioniPrimary (citable) accession number: P33025
    Secondary accession number(s): Q2MAR4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: February 1, 1994
    Last modified: January 20, 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, 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
    4. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries

    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.