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O43172

- PRP4_HUMAN

UniProt

O43172 - PRP4_HUMAN

Protein

U4/U6 small nuclear ribonucleoprotein Prp4

Gene

PRPF4

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 146 (01 Oct 2014)
      Sequence version 2 (02 May 2002)
      Previous versions | rss
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    Functioni

    Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.

    GO - Molecular functioni

    1. protein binding Source: IntAct

    GO - Biological processi

    1. gene expression Source: Reactome
    2. mRNA splicing, via spliceosome Source: BHF-UCL
    3. RNA processing Source: ProtInc
    4. RNA splicing Source: Reactome
    5. RNA splicing, via transesterification reactions Source: UniProtKB

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    Enzyme and pathway databases

    ReactomeiREACT_467. mRNA Splicing - Major Pathway.
    SignaLinkiO43172.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    U4/U6 small nuclear ribonucleoprotein Prp4
    Alternative name(s):
    PRP4 homolog
    Short name:
    hPrp4
    U4/U6 snRNP 60 kDa protein
    WD splicing factor Prp4
    Gene namesi
    Name:PRPF4
    Synonyms:PRP4
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 9

    Organism-specific databases

    HGNCiHGNC:17349. PRPF4.

    Subcellular locationi

    Nucleus speckle By similarity
    Note: Colocalizes with spliceosomal snRNPs.By similarity

    GO - Cellular componenti

    1. Cajal body Source: BHF-UCL
    2. nuclear speck Source: UniProtKB-SubCell
    3. nucleoplasm Source: Reactome
    4. nucleus Source: HPA
    5. spliceosomal complex Source: UniProtKB
    6. U4/U6 snRNP Source: BHF-UCL

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA38448.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 522522U4/U6 small nuclear ribonucleoprotein Prp4PRO_0000051149Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei27 – 271N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiO43172.
    PaxDbiO43172.
    PRIDEiO43172.

    PTM databases

    PhosphoSiteiO43172.

    Expressioni

    Gene expression databases

    ArrayExpressiO43172.
    BgeeiO43172.
    CleanExiHS_PRPF4.
    GenevestigatoriO43172.

    Organism-specific databases

    HPAiHPA021794.
    HPA022248.

    Interactioni

    Subunit structurei

    Interacts directly with PRPF18, PPIH and PRPF3. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39.5 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    GPKOWQ929172EBI-718395,EBI-746309
    PPIHO434472EBI-718395,EBI-1055615

    Protein-protein interaction databases

    BioGridi114576. 69 interactions.
    IntActiO43172. 35 interactions.
    MINTiMINT-270624.
    STRINGi9606.ENSP00000363313.

    Structurei

    Secondary structure

    1
    522
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi108 – 1147
    Beta strandi119 – 1213
    Helixi126 – 13611

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MZWX-ray2.00B107-137[»]
    ProteinModelPortaliO43172.
    SMRiO43172. Positions 107-137, 239-519.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO43172.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Repeati229 – 26840WD 1Add
    BLAST
    Repeati271 – 31848WD 2Add
    BLAST
    Repeati321 – 36040WD 3Add
    BLAST
    Repeati363 – 40240WD 4Add
    BLAST
    Repeati405 – 44440WD 5Add
    BLAST
    Repeati447 – 48741WD 6Add
    BLAST
    Repeati490 – 52132WD 7Add
    BLAST

    Sequence similaritiesi

    Contains 7 WD repeats.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, WD repeat

    Phylogenomic databases

    eggNOGiCOG2319.
    HOGENOMiHOG000157615.
    HOVERGENiHBG030892.
    InParanoidiO43172.
    KOiK12662.
    OMAiHPSRQAY.
    OrthoDBiEOG7P5T0Z.
    PhylomeDBiO43172.
    TreeFamiTF314922.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR020472. G-protein_beta_WD-40_rep.
    IPR027106. Prp4.
    IPR014906. PRP4-like.
    IPR003648. SFM.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR019775. WD40_repeat_CS.
    IPR017986. WD40_repeat_dom.
    [Graphical view]
    PANTHERiPTHR19846. PTHR19846. 1 hit.
    PfamiPF08799. PRP4. 1 hit.
    PF00400. WD40. 7 hits.
    [Graphical view]
    PRINTSiPR00320. GPROTEINBRPT.
    SMARTiSM00500. SFM. 1 hit.
    SM00320. WD40. 7 hits.
    [Graphical view]
    SUPFAMiSSF50978. SSF50978. 1 hit.
    PROSITEiPS00678. WD_REPEATS_1. 2 hits.
    PS50082. WD_REPEATS_2. 6 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: O43172-1) [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

    MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI    50
    LGKDGLKAGI EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN 100
    VSTDDSEVKA CLRALGEPIT LFGEGPAERR ERLRNILSVV GTDALKKTKK 150
    DDEKSKKSKE EYQQTWYHEG PNSLKVARLW IANYSLPRAM KRLEEARLHK 200
    EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS PNSKMLATAC 250
    WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA 300
    ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW 350
    DLEAQEEILH QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI 400
    MFLEGHLKEI YGINFSPNGY HIATGSGDNT CKVWDLRQRR CVYTIPAHQN 450
    LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP GWSPLKTLAG HEGKVMGLDI 500
    SSDGQLIATC SYDRTFKLWM AE 522
    Length:522
    Mass (Da):58,449
    Last modified:May 2, 2002 - v2
    Checksum:i08975A26D0B21857
    GO
    Isoform 2 (identifier: O43172-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         10-10: Missing.

    Show »
    Length:521
    Mass (Da):58,321
    Checksum:iB4EF92D9E12C9188
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti78 – 10326HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261. (PubMed:9328476)CuratedAdd
    BLAST
    Sequence conflicti78 – 781H → R in AAC51925. (PubMed:9404889)Curated
    Sequence conflicti86 – 861V → L in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti134 – 1341R → K in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti141 – 1411G → D in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti176 – 1761Missing in AAC02261. (PubMed:9328476)Curated
    Sequence conflicti275 – 2828NVGAIVFH → KKEQLHSI in AAC02261. (PubMed:9328476)Curated
    Sequence conflicti405 – 4051G → D in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti447 – 4471A → P in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti510 – 5101C → Y in AAB87640. (PubMed:9257651)Curated
    Sequence conflicti521 – 5211A → L in AAB87640. (PubMed:9257651)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei10 – 101Missing in isoform 2. 2 PublicationsVSP_006785

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF001687 Genomic DNA. Translation: AAB87640.1.
    AF016369 mRNA. Translation: AAC51925.1.
    U82756 mRNA. Translation: AAC02261.1.
    AL449305 Genomic DNA. Translation: CAI10968.1.
    CH471090 Genomic DNA. Translation: EAW87362.1.
    BC001588 mRNA. Translation: AAH01588.1.
    BC007424 mRNA. Translation: AAH07424.1.
    CCDSiCCDS59142.1. [O43172-2]
    CCDS6791.1. [O43172-1]
    RefSeqiNP_001231855.1. NM_001244926.1. [O43172-2]
    NP_004688.2. NM_004697.4. [O43172-1]
    UniGeneiHs.744014.

    Genome annotation databases

    EnsembliENST00000374198; ENSP00000363313; ENSG00000136875. [O43172-1]
    ENST00000374199; ENSP00000363315; ENSG00000136875. [O43172-2]
    GeneIDi9128.
    KEGGihsa:9128.
    UCSCiuc004bgx.3. human. [O43172-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF001687 Genomic DNA. Translation: AAB87640.1 .
    AF016369 mRNA. Translation: AAC51925.1 .
    U82756 mRNA. Translation: AAC02261.1 .
    AL449305 Genomic DNA. Translation: CAI10968.1 .
    CH471090 Genomic DNA. Translation: EAW87362.1 .
    BC001588 mRNA. Translation: AAH01588.1 .
    BC007424 mRNA. Translation: AAH07424.1 .
    CCDSi CCDS59142.1. [O43172-2 ]
    CCDS6791.1. [O43172-1 ]
    RefSeqi NP_001231855.1. NM_001244926.1. [O43172-2 ]
    NP_004688.2. NM_004697.4. [O43172-1 ]
    UniGenei Hs.744014.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1MZW X-ray 2.00 B 107-137 [» ]
    ProteinModelPortali O43172.
    SMRi O43172. Positions 107-137, 239-519.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 114576. 69 interactions.
    IntActi O43172. 35 interactions.
    MINTi MINT-270624.
    STRINGi 9606.ENSP00000363313.

    Chemistry

    BindingDBi O43172.
    ChEMBLi CHEMBL1163119.

    PTM databases

    PhosphoSitei O43172.

    Proteomic databases

    MaxQBi O43172.
    PaxDbi O43172.
    PRIDEi O43172.

    Protocols and materials databases

    DNASUi 9128.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000374198 ; ENSP00000363313 ; ENSG00000136875 . [O43172-1 ]
    ENST00000374199 ; ENSP00000363315 ; ENSG00000136875 . [O43172-2 ]
    GeneIDi 9128.
    KEGGi hsa:9128.
    UCSCi uc004bgx.3. human. [O43172-1 ]

    Organism-specific databases

    CTDi 9128.
    GeneCardsi GC09P116037.
    HGNCi HGNC:17349. PRPF4.
    HPAi HPA021794.
    HPA022248.
    MIMi 607795. gene.
    neXtProti NX_O43172.
    PharmGKBi PA38448.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG2319.
    HOGENOMi HOG000157615.
    HOVERGENi HBG030892.
    InParanoidi O43172.
    KOi K12662.
    OMAi HPSRQAY.
    OrthoDBi EOG7P5T0Z.
    PhylomeDBi O43172.
    TreeFami TF314922.

    Enzyme and pathway databases

    Reactomei REACT_467. mRNA Splicing - Major Pathway.
    SignaLinki O43172.

    Miscellaneous databases

    EvolutionaryTracei O43172.
    GeneWikii PRPF4.
    GenomeRNAii 9128.
    NextBioi 34217.
    PROi O43172.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O43172.
    Bgeei O43172.
    CleanExi HS_PRPF4.
    Genevestigatori O43172.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR020472. G-protein_beta_WD-40_rep.
    IPR027106. Prp4.
    IPR014906. PRP4-like.
    IPR003648. SFM.
    IPR015943. WD40/YVTN_repeat-like_dom.
    IPR001680. WD40_repeat.
    IPR019775. WD40_repeat_CS.
    IPR017986. WD40_repeat_dom.
    [Graphical view ]
    PANTHERi PTHR19846. PTHR19846. 1 hit.
    Pfami PF08799. PRP4. 1 hit.
    PF00400. WD40. 7 hits.
    [Graphical view ]
    PRINTSi PR00320. GPROTEINBRPT.
    SMARTi SM00500. SFM. 1 hit.
    SM00320. WD40. 7 hits.
    [Graphical view ]
    SUPFAMi SSF50978. SSF50978. 1 hit.
    PROSITEi PS00678. WD_REPEATS_1. 2 hits.
    PS50082. WD_REPEATS_2. 6 hits.
    PS50294. WD_REPEATS_REGION. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p."
      Lauber J., Plessel G., Prehn S., Will C.L., Fabrizio P., Groning K., Lane W.S., Luehrmann R.
      RNA 3:926-941(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2).
    2. "A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs."
      Horowitz D.S., Kobayashi R., Krainer A.R.
      RNA 3:1374-1387(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 28-38; 58-85; 95-106; 193-200 AND 457-472, INTERACTION WITH U4/U5/U6 SNRNPS.
    3. "Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome."
      Wang A., Forman-Kay J., Luo Y., Luo M., Chow Y.-H., Plumb J., Friesen J.D., Tsui L.-C., Heng H.H.Q., Woolford J.L. Jr., Hu J.
      Hum. Mol. Genet. 6:2117-2126(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH PRPF3 AND U4/U5/U6 SNRNPS.
    4. "DNA sequence and analysis of human chromosome 9."
      Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L.
      , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
      Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Tissue: Colon and Ovary.
    7. "A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor."
      Horowitz D.S., Krainer A.R.
      Genes Dev. 11:139-151(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH PRPF18.
    8. "The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
      Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
      RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT.
    9. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide."
      Reidt U., Wahl M.C., Fasshauer D., Horowitz D.S., Luehrmann R., Ficner R.
      J. Mol. Biol. 331:45-56(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 107-137 IN COMPLEX WITH PPIH.

    Entry informationi

    Entry nameiPRP4_HUMAN
    AccessioniPrimary (citable) accession number: O43172
    Secondary accession number(s): O43445
    , O43864, Q5T1M8, Q96DG2, Q96IK4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 2, 2002
    Last sequence update: May 2, 2002
    Last modified: October 1, 2014
    This is version 146 of the entry and version 2 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, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 9
      Human chromosome 9: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3