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P40615

- DKC1_RAT

UniProt

P40615 - DKC1_RAT

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Protein

H/ACA ribonucleoprotein complex subunit 4

Gene

Dkc1

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Required for telomere maintenance; necessary for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme (By similarity). Also required for ribosome biogenesis. 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.By similarity1 Publication

Catalytic activityi

RNA uridine = RNA pseudouridine.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei126 – 1261NucleophileBy similarity

GO - Molecular functioni

  1. pseudouridine synthase activity Source: InterPro
  2. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. cell proliferation Source: RGD
  2. pseudouridine synthesis Source: InterPro
  3. rRNA processing Source: UniProtKB-KW
Complete GO annotation...

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
Synonyms:Nap57
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Unplaced

Organism-specific databases

RGDi621780. Dkc1.

Subcellular locationi

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

GO - Cellular componenti

  1. Cajal body Source: RGD
  2. nucleolus Source: RGD
  3. nucleoplasm Source: RGD
  4. small nucleolar ribonucleoprotein complex Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 509508H/ACA ribonucleoprotein complex subunit 4PRO_0000121985Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei452 – 4521PhosphoserineBy similarity
Modified residuei454 – 4541PhosphoserineBy similarity
Modified residuei508 – 5081PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiP40615.

PTM databases

PhosphoSiteiP40615.

Expressioni

Gene expression databases

GenevestigatoriP40615.

Interactioni

Subunit structurei

May interact with TERC, which contains a 3'-terminal domain related to the box H/ACA snoRNAs. May interact with the SMN complex, consisting of SMN1 or SMN2, GEMIN2/SIP1, DDX20/GEMIN3, and GEMIN4. 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). 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. Specific interactions with snoRNAs or TERC are mediated by GAR1 and NHP2. Associates with NOLC1/NOPP140. 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

Binary interactionsi

WithEntry#Exp.IntActNotes
LOC100360065D3ZMP64EBI-5746997,EBI-8792072
NAF1Q96HR83EBI-5746997,EBI-2515597From a different organism.

Protein-protein interaction databases

IntActiP40615. 5 interactions.

Structurei

3D structure databases

ProteinModelPortaliP40615.
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 – 2221Nucleolar localizationBy similarityAdd
BLAST
Regioni447 – 50963Nuclear and nucleolar localizationBy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi12 – 187Poly-Lys

Sequence similaritiesi

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

Phylogenomic databases

HOVERGENiHBG081442.
InParanoidiP40615.
KOiK11131.
PhylomeDBiP40615.

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.

P40615-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MADAEAAMTF PKKHKKKKER KPLPEADVAE IQHAEDFLIK PESKAAQLDT
60 70 80 90 100
SQWPLLLKNF DRLNVRTTHY TPIPCGSNPL KREIGEYVRT GFINLDKPSN
110 120 130 140 150
PSSHEVVAWI RRILRVEKTG HSGTLDPKVT GCLIVCIERA TRLVKSQQSA
160 170 180 190 200
GKEYVGVVRL HNAIEGTAQL SRALETLTGA LFQRPPLIAA VKRQLRVRTI
210 220 230 240 250
YESRVVEYDP ERRLGVFWVS CEAGTYIRTL CVHLGLLLGV GGQMQELRRV
260 270 280 290 300
RSGVVGERDH MVTMHDVLDA QYLYDHHRDE SYLRRVVFPL EKLLTSHKRL
310 320 330 340 350
VMKDSAVNAI CYGAKIMLPG LLRYEDGIEV NQEVVVITTK GEAVCVAIAL
360 370 380 390 400
MTTAVISTCD HGVVAKIKRV IMERDTYPRK WGLGPKASQK KQLIKQGLLD
410 420 430 440 450
KHGRPTDGTP ASWTRDYVDY SDSSKKATAA EATPGPGVTA DAASIVKRKR
460 470 480 490 500
DSDSDADEAT PTTTPRVKKE KKKKKEKADG GEEAAEDGDG DATRKKKKKK

ARAAEELSG
Length:509
Mass (Da):56,615
Last modified:January 23, 2007 - v4
Checksum:i038862EBBF2A1E2F
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti459 – 50850ATPTT…AEELS → RRPLPRP AA sequence (PubMed:7798307)CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z34922 mRNA. Translation: CAA84402.1.
BC099832 mRNA. Translation: AAH99832.1.
PIRiA55163.
RefSeqiNP_596910.1. NM_133419.1.
UniGeneiRn.4223.

Genome annotation databases

GeneIDi170944.
KEGGirno:170944.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z34922 mRNA. Translation: CAA84402.1 .
BC099832 mRNA. Translation: AAH99832.1 .
PIRi A55163.
RefSeqi NP_596910.1. NM_133419.1.
UniGenei Rn.4223.

3D structure databases

ProteinModelPortali P40615.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P40615. 5 interactions.

PTM databases

PhosphoSitei P40615.

Proteomic databases

PRIDEi P40615.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 170944.
KEGGi rno:170944.

Organism-specific databases

CTDi 1736.
RGDi 621780. Dkc1.

Phylogenomic databases

HOVERGENi HBG081442.
InParanoidi P40615.
KOi K11131.
PhylomeDBi P40615.

Miscellaneous databases

NextBioi 621465.
PROi P40615.

Gene expression databases

Genevestigatori P40615.

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

« Hide 'large scale' publications
  1. "NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria."
    Meier U., Blobel G.
    J. Cell Biol. 127:1505-1514(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PROTEIN SEQUENCE OF 21-43; 83-96 AND 98-119, SUBCELLULAR LOCATION, INTERACTION WITH NOLC1.
    Tissue: Liver.
  2. Meier U.
    Submitted (DEC-1997) to UniProtKB
    Cited for: SEQUENCE REVISION TO C-TERMINUS.
  3. "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].
    Tissue: Prostate.
  4. "Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140."
    Wang C., Query C.C., Meier U.T.
    Mol. Cell. Biol. 22:8457-8466(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH GAR1; NHP2; NOP10 AND NOLC1, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiDKC1_RAT
AccessioniPrimary (citable) accession number: P40615
Secondary accession number(s): Q499M9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: October 29, 2014
This is version 109 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, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3