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Q9ESX5

- DKC1_MOUSE

UniProt

Q9ESX5 - DKC1_MOUSE

Protein

H/ACA ribonucleoprotein complex subunit 4

Gene

Dkc1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 4 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme.2 Publications

    Catalytic activityi

    RNA uridine = RNA pseudouridine.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei125 – 1251NucleophileBy similarity

    GO - Molecular functioni

    1. pseudouridine synthase activity Source: InterPro
    2. pseudouridylate synthase activity Source: MGI
    3. RNA binding Source: MGI
    4. snoRNP binding Source: MGI
    5. telomerase activity Source: Ensembl

    GO - Biological processi

    1. RNA processing Source: MGI
    2. rRNA modification Source: MGI

    Keywords - Molecular functioni

    Isomerase, Ribonucleoprotein

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing

    Keywords - Ligandi

    RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    H/ACA ribonucleoprotein complex subunit 4 (EC:5.4.99.-)
    Alternative name(s):
    Dyskerin
    Nopp140-associated protein of 57 kDa
    Nucleolar protein NAP57
    Nucleolar protein family A member 4
    snoRNP protein DKC1
    Gene namesi
    Name:Dkc1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome X

    Organism-specific databases

    MGIiMGI:1861727. Dkc1.

    Subcellular locationi

    Nucleusnucleolus. NucleusCajal body
    Note: Also localized to Cajal bodies (coiled bodies).

    GO - Cellular componenti

    1. Cajal body Source: UniProtKB-SubCell
    2. nucleolus Source: MGI
    3. telomerase holoenzyme complex Source: Ensembl

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi353 – 3531A → V: Destabilization of TERC, impaired telomerase function, and reduced rRNA pseudouridylation and pre-rRNA processing. 1 Publication
    Mutagenesisi402 – 4021G → E: Reduced rRNA pseudouridylation and pre-rRNA processing. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 509508H/ACA ribonucleoprotein complex subunit 4PRO_0000121984Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanineBy similarity
    Modified residuei451 – 4511Phosphoserine3 Publications
    Modified residuei453 – 4531Phosphoserine3 Publications
    Modified residuei455 – 4551Phosphoserine2 Publications
    Modified residuei481 – 4811Phosphoserine1 Publication
    Modified residuei508 – 5081Phosphoserine3 Publications

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9ESX5.
    PaxDbiQ9ESX5.
    PRIDEiQ9ESX5.

    PTM databases

    PhosphoSiteiQ9ESX5.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed, with elevated levels in Purkinje cells, the olfactory bulb, and Leydig cells of the testis.1 Publication

    Developmental stagei

    Expressed throughout development, particularly in developing epithelial tissues.1 Publication

    Gene expression databases

    ArrayExpressiQ9ESX5.
    BgeeiQ9ESX5.
    GenevestigatoriQ9ESX5.

    Interactioni

    Subunit structurei

    Part of the H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which contains NHP2/NOLA2, GAR1/NOLA1, NOP10/NOLA3, and DKC1/NOLA4, which is presumed to be the catalytic subunit. The complex contains a stable core formed by binding of one or two NOP10-DKC1 heterodimers to NHP2; GAR1 subsequently binds to this core via DKC1. The complex binds a box H/ACA small nucleolar RNA (snoRNA), which may target the specific site of modification within the RNA substrate. During assembly, the complex contains NAF1 instead of GAR1/NOLA1. The complex also interacts with TERC, which contains a 3'-terminal domain related to the box H/ACA snoRNAs. Specific interactions with snoRNAs or TERC are mediated by GAR1 and NHP2. Associates with NOLC1/NOPP140. H/ACA snoRNPs interact with the SMN complex, consisting of SMN1 or SMN2, GEMIN2/SIP1, DDX20/GEMIN3, and GEMIN4. This is mediated by interaction between GAR1 and SMN1 or SMN2. The SMN complex may be required for correct assembly of the H/ACA snoRNP complex. Component of the telomerase holoenzyme complex at least composed of TERT, DKC1, WRAP53/TCAB1, NOP10, NHP2, GAR1, TEP1, EST1A, POT1 and a telomerase RNA template component (TERC) By similarity. Interacts with SHQ1; this interaction may lead to the stabilization of DKC1, from the time of its synthesis until its association with NOP10, NHP2, and NAF1 at the nascent H/ACA RNA By similarity.By similarity

    Protein-protein interaction databases

    BioGridi232777. 1 interaction.
    IntActiQ9ESX5. 3 interactions.
    MINTiMINT-1854010.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9ESX5.
    SMRiQ9ESX5. Positions 48-408.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini297 – 37276PUAPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 2120Nucleolar localizationBy similarityAdd
    BLAST
    Regioni446 – 50964Nuclear and nucleolar localizationBy similarityAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi11 – 177Poly-Lys

    Sequence similaritiesi

    Belongs to the pseudouridine synthase TruB family.Curated
    Contains 1 PUA domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0130.
    GeneTreeiENSGT00510000047092.
    HOGENOMiHOG000231224.
    HOVERGENiHBG081442.
    InParanoidiQ3UWE5.
    KOiK11131.
    OMAiHDKLPGG.
    OrthoDBiEOG7QC7W0.
    TreeFamiTF300354.

    Family and domain databases

    Gene3Di2.30.130.10. 1 hit.
    InterProiIPR012960. Dyskerin-like.
    IPR002501. PsdUridine_synth.
    IPR020103. PsdUridine_synth_cat_dom.
    IPR002478. PUA.
    IPR015947. PUA-like_domain.
    IPR004802. tRNA_PsdUridine_synth_B_fam.
    IPR004521. Uncharacterised_CHP00451.
    [Graphical view]
    PANTHERiPTHR23127. PTHR23127. 1 hit.
    PfamiPF08068. DKCLD. 1 hit.
    PF01472. PUA. 1 hit.
    PF01509. TruB_N. 1 hit.
    [Graphical view]
    SMARTiSM00359. PUA. 1 hit.
    [Graphical view]
    SUPFAMiSSF55120. SSF55120. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsiTIGR00425. CBF5. 1 hit.
    TIGR00451. unchar_dom_2. 1 hit.
    PROSITEiPS50890. PUA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9ESX5-1 [UniParc]FASTAAdd to Basket

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    MADAEVITFP KKHKKKKDRK PLQEDDVAEI QHAEEFLIKP ESKVAQLDTS    50
    QWPLLLKNFD KLNVRTAHYT PLPCGSNPLK REIGDYIRTG FINLDKPSNP 100
    SSHEVVAWIR RILRVEKTGH SGTLDPKVTG CLIVCIERAT RLVKSQQSAG 150
    KEYVGIVRLH NAIEGGTQLS RALETLTGAL FQRPPLIAAV KRQLRVRTIY 200
    ESKMIEYDPE RRLGIFWVSC EAGTYIRTLC VHLGLLLGVG GQMQELRRVR 250
    SGVMSEKDHM VTMHDVLDAQ WLYDNHKDES YLRRVVYPLE KLLTSHKRLV 300
    MKDSAVNAIC YGAKIMLPGL LRYEDGIEVN QEIVVITTKG EAICMAIALM 350
    TTAVISTCDH GIVAKIKRVI MERDTYPRKW GLGPKASQKK MMIKQGLLDK 400
    HGKPTDNTPA TWKQDYIDYS DSGKNTLVTE AVQAPQLAAE AVNVIKRKRD 450
    SESESDETPT VPQLKEKKKK KDKKPKTVLE SGGETGDGDN DTTKKKKKKK 500
    VKVVEEMSE 509
    Length:509
    Mass (Da):57,402
    Last modified:July 27, 2011 - v4
    Checksum:i17C50FDF48912A14
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti234 – 2418GLLLGVGG → CFVLGSGC in CAC04528. (PubMed:10903840)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ250973
    , AJ250972, AJ250974, AJ250975, AJ250976, AJ250978, AJ250980, AJ250981, AJ250979, AJ250977 Genomic DNA. Translation: CAC04528.1.
    AK136418 mRNA. Translation: BAE22970.1.
    AL808110 Genomic DNA. Translation: CAM26485.1.
    CCDSiCCDS41029.1.
    RefSeqiNP_001025478.1. NM_001030307.2.
    UniGeneiMm.291062.

    Genome annotation databases

    EnsembliENSMUST00000033776; ENSMUSP00000033776; ENSMUSG00000031403.
    GeneIDi245474.
    KEGGimmu:245474.
    UCSCiuc009tpo.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ250973
    , AJ250972 , AJ250974 , AJ250975 , AJ250976 , AJ250978 , AJ250980 , AJ250981 , AJ250979 , AJ250977 Genomic DNA. Translation: CAC04528.1 .
    AK136418 mRNA. Translation: BAE22970.1 .
    AL808110 Genomic DNA. Translation: CAM26485.1 .
    CCDSi CCDS41029.1.
    RefSeqi NP_001025478.1. NM_001030307.2.
    UniGenei Mm.291062.

    3D structure databases

    ProteinModelPortali Q9ESX5.
    SMRi Q9ESX5. Positions 48-408.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 232777. 1 interaction.
    IntActi Q9ESX5. 3 interactions.
    MINTi MINT-1854010.

    PTM databases

    PhosphoSitei Q9ESX5.

    Proteomic databases

    MaxQBi Q9ESX5.
    PaxDbi Q9ESX5.
    PRIDEi Q9ESX5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000033776 ; ENSMUSP00000033776 ; ENSMUSG00000031403 .
    GeneIDi 245474.
    KEGGi mmu:245474.
    UCSCi uc009tpo.2. mouse.

    Organism-specific databases

    CTDi 1736.
    MGIi MGI:1861727. Dkc1.

    Phylogenomic databases

    eggNOGi COG0130.
    GeneTreei ENSGT00510000047092.
    HOGENOMi HOG000231224.
    HOVERGENi HBG081442.
    InParanoidi Q3UWE5.
    KOi K11131.
    OMAi HDKLPGG.
    OrthoDBi EOG7QC7W0.
    TreeFami TF300354.

    Miscellaneous databases

    NextBioi 386727.
    PROi Q9ESX5.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9ESX5.
    Bgeei Q9ESX5.
    Genevestigatori Q9ESX5.

    Family and domain databases

    Gene3Di 2.30.130.10. 1 hit.
    InterProi IPR012960. Dyskerin-like.
    IPR002501. PsdUridine_synth.
    IPR020103. PsdUridine_synth_cat_dom.
    IPR002478. PUA.
    IPR015947. PUA-like_domain.
    IPR004802. tRNA_PsdUridine_synth_B_fam.
    IPR004521. Uncharacterised_CHP00451.
    [Graphical view ]
    PANTHERi PTHR23127. PTHR23127. 1 hit.
    Pfami PF08068. DKCLD. 1 hit.
    PF01472. PUA. 1 hit.
    PF01509. TruB_N. 1 hit.
    [Graphical view ]
    SMARTi SM00359. PUA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55120. SSF55120. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsi TIGR00425. CBF5. 1 hit.
    TIGR00451. unchar_dom_2. 1 hit.
    PROSITEi PS50890. PUA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Gene structure and expression of the mouse dyskeratosis congenita gene, dkc1."
      Heiss N.S., Baechner D., Salowsky R., Kolb A., Kioschis P., Poustka A.
      Genomics 67:153-163(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
      Strain: 129/Ola.
    2. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J.
      Tissue: Colon.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: C57BL/6J.
    4. "Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification."
      Ruggero D., Grisendi S., Piazza F., Rego E., Mari F., Rao P.H., Cordon-Cardo C., Pandolfi P.P.
      Science 299:259-262(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "Mouse dyskerin mutations affect accumulation of telomerase RNA and small nucleolar RNA, telomerase activity, and ribosomal RNA processing."
      Mochizuki Y., He J., Kulkarni S., Bessler M., Mason P.J.
      Proc. Natl. Acad. Sci. U.S.A. 101:10756-10761(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF ALA-353 AND GLY-402.
    6. "Comprehensive identification of phosphorylation sites in postsynaptic density preparations."
      Trinidad J.C., Specht C.G., Thalhammer A., Schoepfer R., Burlingame A.L.
      Mol. Cell. Proteomics 5:914-922(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-508, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Brain.
    7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-451; SER-453 AND SER-481, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    8. "Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis."
      Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.
      J. Proteome Res. 7:3957-3967(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-451; SER-453 AND SER-455, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    9. "The phagosomal proteome in interferon-gamma-activated macrophages."
      Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
      Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-508, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry."
      Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.
      Mol. Cell. Proteomics 8:904-912(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-451; SER-453; SER-455 AND SER-508, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Embryonic fibroblast.

    Entry informationi

    Entry nameiDKC1_MOUSE
    AccessioniPrimary (citable) accession number: Q9ESX5
    Secondary accession number(s): Q3UWE5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 111 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3