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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

Manual assertion based on experiment ini

  • Ref.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.

  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)DescriptionActionsGraphical viewLength
    Active sitei31Proton donor1 PublicationUniRule annotation1
    Binding sitei93SubstrateUniRule annotation1 Publication1
    Binding sitei113Substrate; via amide nitrogenUniRule annotation1 Publication1
    Metal bindingi145ManganeseUniRule annotation1 Publication1
    Active sitei166Nucleophile1 PublicationUniRule annotation1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12033. psuG.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi31E → A: 7500-fold decrease in reaction rate while little change in substrate affinity. 1 Publication1
    Mutagenesisi93K → A: 17-fold decrease in reaction rate while modest decrease in substrate affinity. 1 Publication1
    Mutagenesisi149D → A: Loss of activity. 1 Publication1
    Mutagenesisi166K → A: 2900-fold decrease in reaction rate while no change in substrate affinity. 1 Publication1
    Mutagenesisi289N → A: 17-fold decrease in reaction rate while modest decrease in substrate affinity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001691501 – 312Pseudouridine-5'-phosphate glycosidaseAdd BLAST312

    Proteomic databases

    PaxDbiP33025.
    PRIDEiP33025.

    Interactioni

    Subunit structurei

    Homotrimer.UniRule annotation1 Publication

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1312
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Turni8 – 10Combined sources3
    Beta strandi11 – 13Combined sources3
    Helixi15 – 22Combined sources8
    Beta strandi27 – 30Combined sources4
    Helixi33 – 36Combined sources4
    Helixi43 – 57Combined sources15
    Beta strandi61 – 68Combined sources8
    Beta strandi71 – 75Combined sources5
    Helixi78 – 87Combined sources10
    Helixi88 – 90Combined sources3
    Beta strandi91 – 94Combined sources4
    Turni96 – 98Combined sources3
    Helixi99 – 104Combined sources6
    Beta strandi109 – 111Combined sources3
    Helixi113 – 122Combined sources10
    Beta strandi127 – 129Combined sources3
    Helixi140 – 143Combined sources4
    Helixi148 – 155Combined sources8
    Beta strandi159 – 162Combined sources4
    Helixi171 – 180Combined sources10
    Beta strandi185 – 189Combined sources5
    Beta strandi202 – 204Combined sources3
    Beta strandi206 – 209Combined sources4
    Helixi212 – 224Combined sources13
    Beta strandi231 – 234Combined sources4
    Helixi239 – 241Combined sources3
    Helixi245 – 262Combined sources18
    Helixi266 – 268Combined sources3
    Helixi269 – 280Combined sources12
    Turni281 – 283Combined sources3
    Helixi284 – 310Combined sources27

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni147 – 149Substrate bindingUniRule annotation1 Publication3

    Sequence similaritiesi

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

    Phylogenomic databases

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

    Family and domain databases

    HAMAPiMF_01876. PsiMP_glycosidase. 1 hit.
    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP33025.
    PRIDEiP33025.

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

    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: November 2, 2016
    This is version 118 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.