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Protein

H/ACA ribonucleoprotein complex subunit 4

Gene

Dkc1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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. poly(A) RNA binding Source: MGI
  2. pseudouridine synthase activity Source: InterPro
  3. pseudouridylate synthase activity Source: MGI
  4. RNA binding Source: MGI
  5. snoRNP binding Source: MGI
  6. telomerase activity Source: MGI

GO - Biological processi

  1. RNA-dependent DNA replication Source: GOC
  2. RNA processing Source: MGI
  3. rRNA modification Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Ribonucleoprotein

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_262572. Telomere Extension By Telomerase.

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. nucleus Source: MGI
  4. telomerase holoenzyme complex Source: MGI
Complete GO annotation...

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

BgeeiQ9ESX5.
ExpressionAtlasiQ9ESX5. baseline and differential.
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.
InParanoidiQ9ESX5.
KOiK11131.
OMAiAVEMSSC.
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

« Hide

        10         20         30         40         50
MADAEVITFP KKHKKKKDRK PLQEDDVAEI QHAEEFLIKP ESKVAQLDTS
60 70 80 90 100
QWPLLLKNFD KLNVRTAHYT PLPCGSNPLK REIGDYIRTG FINLDKPSNP
110 120 130 140 150
SSHEVVAWIR RILRVEKTGH SGTLDPKVTG CLIVCIERAT RLVKSQQSAG
160 170 180 190 200
KEYVGIVRLH NAIEGGTQLS RALETLTGAL FQRPPLIAAV KRQLRVRTIY
210 220 230 240 250
ESKMIEYDPE RRLGIFWVSC EAGTYIRTLC VHLGLLLGVG GQMQELRRVR
260 270 280 290 300
SGVMSEKDHM VTMHDVLDAQ WLYDNHKDES YLRRVVYPLE KLLTSHKRLV
310 320 330 340 350
MKDSAVNAIC YGAKIMLPGL LRYEDGIEVN QEIVVITTKG EAICMAIALM
360 370 380 390 400
TTAVISTCDH GIVAKIKRVI MERDTYPRKW GLGPKASQKK MMIKQGLLDK
410 420 430 440 450
HGKPTDNTPA TWKQDYIDYS DSGKNTLVTE AVQAPQLAAE AVNVIKRKRD
460 470 480 490 500
SESESDETPT VPQLKEKKKK KDKKPKTVLE SGGETGDGDN DTTKKKKKKK

VKVVEEMSE
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

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

PTM databases

PhosphoSiteiQ9ESX5.

Proteomic databases

MaxQBiQ9ESX5.
PaxDbiQ9ESX5.
PRIDEiQ9ESX5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi1736.
MGIiMGI:1861727. Dkc1.

Phylogenomic databases

eggNOGiCOG0130.
GeneTreeiENSGT00510000047092.
HOGENOMiHOG000231224.
HOVERGENiHBG081442.
InParanoidiQ9ESX5.
KOiK11131.
OMAiAVEMSSC.
OrthoDBiEOG7QC7W0.
TreeFamiTF300354.

Enzyme and pathway databases

ReactomeiREACT_262572. Telomere Extension By Telomerase.

Miscellaneous databases

NextBioi386727.
PROiQ9ESX5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9ESX5.
ExpressionAtlasiQ9ESX5. baseline and differential.
GenevestigatoriQ9ESX5.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: February 4, 2015
This is version 115 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

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 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.