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Protein

Pseudouridine-5'-phosphatase

Gene

PUDP

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.1 Publication

Catalytic activityi

Pseudouridine 5'-phosphate + H2O = pseudouridine + phosphate.1 Publication

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=0.38 µM for 5'-PsiMP1 Publication
  2. KM=1.5 mM for 3'-AMP1 Publication
  3. KM=5.9 mM for Fructose-6-P1 Publication
  4. KM=9.4 mM for 5'-UMP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei14NucleophileBy similarity1
    Metal bindingi14MagnesiumBy similarity1
    Active sitei16Proton donorBy similarity1
    Metal bindingi16MagnesiumBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Nucleotide metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000130021-MONOMER.
    ReactomeiR-HSA-73614. Pyrimidine salvage reactions.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pseudouridine-5'-phosphataseImported (EC:3.1.3.96)
    Alternative name(s):
    Haloacid dehalogenase-like hydrolase domain-containing protein 1
    Haloacid dehalogenase-like hydrolase domain-containing protein 1A
    Protein GS1
    Pseudouridine-5'-monophosphatase
    Short name:
    5'-PsiMPase
    Gene namesi
    Name:PUDPImported
    Synonyms:DXF68S1E, FAM16AX, GS1, HDHD1, HDHD1A
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome X

    Organism-specific databases

    HGNCiHGNC:16818. PUDP.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: GO_Central
    • cytosol Source: Reactome
    • extracellular exosome Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Organism-specific databases

    DisGeNETi8226.
    OpenTargetsiENSG00000130021.
    PharmGKBiPA165756731.

    Polymorphism and mutation databases

    BioMutaiHDHD1.
    DMDMi269849688.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001080681 – 228Pseudouridine-5'-phosphataseAdd BLAST228

    Proteomic databases

    EPDiQ08623.
    MaxQBiQ08623.
    PeptideAtlasiQ08623.
    PRIDEiQ08623.

    PTM databases

    DEPODiQ08623.
    iPTMnetiQ08623.
    PhosphoSitePlusiQ08623.

    Expressioni

    Inductioni

    Inhibited by low concentrations of calcium.

    Gene expression databases

    BgeeiENSG00000130021.
    CleanExiHS_HDHD1A.
    ExpressionAtlasiQ08623. baseline and differential.
    GenevisibleiQ08623. HS.

    Interactioni

    Protein-protein interaction databases

    BioGridi113859. 10 interactors.
    MINTiMINT-5003687.

    Structurei

    Secondary structure

    1228
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi1 – 3Combined sources3
    Beta strandi9 – 14Combined sources6
    Turni17 – 19Combined sources3
    Helixi22 – 36Combined sources15
    Helixi43 – 49Combined sources7
    Helixi54 – 65Combined sources12
    Helixi71 – 85Combined sources15
    Helixi86 – 88Combined sources3
    Helixi95 – 104Combined sources10
    Beta strandi109 – 112Combined sources4
    Helixi117 – 123Combined sources7
    Turni124 – 126Combined sources3
    Helixi128 – 131Combined sources4
    Helixi153 – 160Combined sources8
    Beta strandi162 – 164Combined sources3
    Helixi168 – 170Combined sources3
    Beta strandi171 – 177Combined sources7
    Helixi178 – 186Combined sources9
    Beta strandi190 – 193Combined sources4
    Helixi201 – 203Combined sources3
    Beta strandi207 – 210Combined sources4
    Helixi214 – 216Combined sources3
    Helixi219 – 222Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3L5KX-ray2.00A1-228[»]
    ProteinModelPortaliQ08623.
    SMRiQ08623.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ08623.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00390000014753.
    HOGENOMiHOG000248341.
    HOVERGENiHBG005917.
    KOiK17623.
    OMAiDSPFGVT.
    OrthoDBiEOG091G0I8V.
    PhylomeDBiQ08623.
    TreeFamiTF105946.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q08623-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MAAPPQPVTH LIFDMDGLLL DTERLYSVVF QEICNRYDKK YSWDVKSLVM
    60 70 80 90 100
    GKKALEAAQI IIDVLQLPMS KEELVEESQT KLKEVFPTAA LMPGAEKLII
    110 120 130 140 150
    HLRKHGIPFA LATSSGSASF DMKTSRHKEF FSLFSHIVLG DDPEVQHGKP
    160 170 180 190 200
    DPDIFLACAK RFSPPPAMEK CLVFEDAPNG VEAALAAGMQ VVMVPDGNLS
    210 220
    RDLTTKATLV LNSLQDFQPE LFGLPSYE
    Length:228
    Mass (Da):25,249
    Last modified:November 24, 2009 - v3
    Checksum:iEF9B8CC51C122924
    GO
    Isoform 2 (identifier: Q08623-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         51-93: Missing.

    Note: No experimental confirmation available.
    Show »
    Length:185
    Mass (Da):20,529
    Checksum:i6AEAE431AC9D25BB
    GO
    Isoform 3 (identifier: Q08623-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         171-228: CLVFEDAPNG...PELFGLPSYE → SSIHRPRLLT...NQLLLCSDDT

    Note: No experimental confirmation available.Curated
    Show »
    Length:208
    Mass (Da):23,283
    Checksum:i9BE317B82AA8FF15
    GO
    Isoform 4 (identifier: Q08623-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         20-20: L → LGYTGSIVAAASGESSRGLQSRWT

    Note: No experimental confirmation available.
    Show »
    Length:251
    Mass (Da):27,573
    Checksum:i8671CFD416181D12
    GO

    Sequence cautioni

    The sequence AAA58622 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
    The sequence AAH12494 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
    The sequence BAD97125 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
    The sequence BAG35973 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti116G → R in AAH12494 (PubMed:15489334).Curated1
    Sequence conflicti153D → G in BAD97125 (PubMed:14702039).Curated1
    Sequence conflicti191V → A in AAA58622 (PubMed:1284467).Curated1
    Isoform 3 (identifier: Q08623-3)
    Sequence conflicti198C → S in BAH13339 (PubMed:14702039).Curated1

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_06109488T → M.2 PublicationsCorresponds to variant rs1131197dbSNPEnsembl.1
    Natural variantiVAR_060625165P → A.Corresponds to variant rs3747386dbSNPEnsembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_04480420L → LGYTGSIVAAASGESSRGLQ SRWT in isoform 4. 1 Publication1
    Alternative sequenceiVSP_04002951 – 93Missing in isoform 2. 1 PublicationAdd BLAST43
    Alternative sequenceiVSP_042020171 – 228CLVFE…LPSYE → SSIHRPRLLTAQKCQGCRDP FSALLLLCNQLLLCSDDT in isoform 3. 1 PublicationAdd BLAST58

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK300985 mRNA. Translation: BAG62605.1.
    AK313155 mRNA. Translation: BAG35973.1. Different initiation.
    AK223405 mRNA. Translation: BAD97125.1. Different initiation.
    AK300740 mRNA. Translation: BAH13339.1.
    AC073583 Genomic DNA. No translation available.
    CH471074 Genomic DNA. Translation: EAW98748.1.
    BC012494 mRNA. Translation: AAH12494.1. Different initiation.
    DR156836 mRNA. No translation available.
    M86934 mRNA. Translation: AAA58622.1. Different initiation.
    CCDSiCCDS48075.1. [Q08623-1]
    CCDS48076.1. [Q08623-4]
    CCDS55366.1. [Q08623-3]
    CCDS55367.1. [Q08623-2]
    RefSeqiNP_001129037.1. NM_001135565.1. [Q08623-4]
    NP_001171606.1. NM_001178135.1. [Q08623-3]
    NP_001171607.1. NM_001178136.1. [Q08623-2]
    NP_036212.3. NM_012080.4. [Q08623-1]
    UniGeneiHs.185910.

    Genome annotation databases

    EnsembliENST00000381077; ENSP00000370467; ENSG00000130021. [Q08623-1]
    ENST00000412827; ENSP00000406260; ENSG00000130021. [Q08623-2]
    ENST00000424830; ENSP00000396452; ENSG00000130021. [Q08623-4]
    ENST00000540122; ENSP00000441208; ENSG00000130021. [Q08623-3]
    GeneIDi8226.
    KEGGihsa:8226.
    UCSCiuc004crv.2. human. [Q08623-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AK300985 mRNA. Translation: BAG62605.1.
    AK313155 mRNA. Translation: BAG35973.1. Different initiation.
    AK223405 mRNA. Translation: BAD97125.1. Different initiation.
    AK300740 mRNA. Translation: BAH13339.1.
    AC073583 Genomic DNA. No translation available.
    CH471074 Genomic DNA. Translation: EAW98748.1.
    BC012494 mRNA. Translation: AAH12494.1. Different initiation.
    DR156836 mRNA. No translation available.
    M86934 mRNA. Translation: AAA58622.1. Different initiation.
    CCDSiCCDS48075.1. [Q08623-1]
    CCDS48076.1. [Q08623-4]
    CCDS55366.1. [Q08623-3]
    CCDS55367.1. [Q08623-2]
    RefSeqiNP_001129037.1. NM_001135565.1. [Q08623-4]
    NP_001171606.1. NM_001178135.1. [Q08623-3]
    NP_001171607.1. NM_001178136.1. [Q08623-2]
    NP_036212.3. NM_012080.4. [Q08623-1]
    UniGeneiHs.185910.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3L5KX-ray2.00A1-228[»]
    ProteinModelPortaliQ08623.
    SMRiQ08623.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi113859. 10 interactors.
    MINTiMINT-5003687.

    PTM databases

    DEPODiQ08623.
    iPTMnetiQ08623.
    PhosphoSitePlusiQ08623.

    Polymorphism and mutation databases

    BioMutaiHDHD1.
    DMDMi269849688.

    Proteomic databases

    EPDiQ08623.
    MaxQBiQ08623.
    PeptideAtlasiQ08623.
    PRIDEiQ08623.

    Protocols and materials databases

    DNASUi8226.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000381077; ENSP00000370467; ENSG00000130021. [Q08623-1]
    ENST00000412827; ENSP00000406260; ENSG00000130021. [Q08623-2]
    ENST00000424830; ENSP00000396452; ENSG00000130021. [Q08623-4]
    ENST00000540122; ENSP00000441208; ENSG00000130021. [Q08623-3]
    GeneIDi8226.
    KEGGihsa:8226.
    UCSCiuc004crv.2. human. [Q08623-1]

    Organism-specific databases

    CTDi8226.
    DisGeNETi8226.
    GeneCardsiHDHD1.
    HGNCiHGNC:16818. PUDP.
    MIMi306480. gene.
    neXtProtiNX_Q08623.
    OpenTargetsiENSG00000130021.
    PharmGKBiPA165756731.
    GenAtlasiSearch...

    Phylogenomic databases

    GeneTreeiENSGT00390000014753.
    HOGENOMiHOG000248341.
    HOVERGENiHBG005917.
    KOiK17623.
    OMAiDSPFGVT.
    OrthoDBiEOG091G0I8V.
    PhylomeDBiQ08623.
    TreeFamiTF105946.

    Enzyme and pathway databases

    BioCyciZFISH:ENSG00000130021-MONOMER.
    ReactomeiR-HSA-73614. Pyrimidine salvage reactions.

    Miscellaneous databases

    EvolutionaryTraceiQ08623.
    GeneWikiiHDHD1A.
    GenomeRNAii8226.
    PROiQ08623.
    SOURCEiSearch...

    Gene expression databases

    BgeeiENSG00000130021.
    CleanExiHS_HDHD1A.
    ExpressionAtlasiQ08623. baseline and differential.
    GenevisibleiQ08623. HS.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiHDHD1_HUMAN
    AccessioniPrimary (citable) accession number: Q08623
    Secondary accession number(s): B2R7X6
    , B4DV93, B7Z6Q3, E9PAV8, F5GWZ2, Q53F84, Q96EB8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: November 24, 2009
    Last modified: November 2, 2016
    This is version 138 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. 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.