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Protein

Pre-mRNA-processing factor 19

Gene

Prpf19

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

Functioni

Ubiquitin-protein ligase which is a core component of several complexes mainly involved pre-mRNA splicing and DNA repair. Core component of the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome and participates in its assembly, its remodeling and is required for its activity. During assembly of the spliceosome, mediates 'Lys-63'-linked polyubiquitination of the U4 spliceosomal protein PRPF3. Ubiquitination of PRPF3 allows its recognition by the U5 component PRPF8 and stabilizes the U4/U5/U6 tri-snRNP spliceosomal complex. Recruited to RNA polymerase II C-terminal domain (CTD) and the pre-mRNA, it may also couple the transcriptional and spliceosomal machineries. The XAB2 complex, which contains PRPF19, is also involved in pre-mRNA splicing, transcription and transcription-coupled repair. Beside its role in pre-mRNA splicing PRPF19, as part of the PRP19-CDC5L complex, plays a role in the DNA damage response/DDR. It is recruited to the sites of DNA damage by the RPA complex where PRPF19 directly ubiquitinates RPA1 and RPA2. 'Lys-63'-linked polyubiquitination of the RPA complex allows the recruitment of the ATR-ATRIP complex and the activation of ATR, a master regulator of the DNA damage response. May also play a role in DNA double-strand break (DSB) repair by recruiting the repair factor SETMAR to altered DNA. As part of the PSO4 complex may also be involved in the DNA interstrand cross-links/ICLs repair process. In addition, may also mediate 'Lys-48'-linked polyubiquitination of substrates and play a role in proteasomal degradation (By similarity). May play a role in the biogenesis of lipid droplets (By similarity). May play a role in neural differentiation possibly through its function as part of the spliceosome (PubMed:16352598).By similarity1 Publication

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.By similarity
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, mRNA processing, mRNA splicing, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiR-RNO-6781823. Formation of TC-NER Pre-Incision Complex.
R-RNO-6782135. Dual incision in TC-NER.
R-RNO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-RNO-72163. mRNA Splicing - Major Pathway.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing factor 19Curated (EC:6.3.2.-By similarity)
Alternative name(s):
Neuronal differentiation-related gene protein
PRP19/PSO4 homolog
Gene namesi
Name:Prpf19Imported
Synonyms:Prp19
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 1

Organism-specific databases

RGDi708496. Prpf19.

Subcellular locationi

  • Nucleus 1 Publication
  • Nucleusnucleoplasm By similarity
  • Cytoplasmcytoskeletonspindle By similarity
  • Cytoplasm By similarity
  • Lipid droplet By similarity

  • Note: Nucleoplasmic in interphase cells. Irregularly distributed in anaphase cells. In prophase cells, uniformly distributed, but not associated with condensing chromosomes. Found in extrachromosomal regions in metaphase cells. Mainly localized to the mitotic spindle apparatus when chromosomes segregate during anaphase. When nuclei reform during late telophase, uniformly distributed in daughter cells and displays no preferred association with decondensing chromatin. Recruited on damaged DNA at sites of double-strand break (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Lipid droplet, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 504503Pre-mRNA-processing factor 19PRO_0000051147Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei122 – 1221N6-acetyllysineBy similarity
Modified residuei179 – 1791N6-acetyllysineBy similarity
Modified residuei244 – 2441N6-acetyllysineBy similarity
Modified residuei261 – 2611N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ9JMJ4.
PeptideAtlasiQ9JMJ4.
PRIDEiQ9JMJ4.

PTM databases

iPTMnetiQ9JMJ4.
PhosphoSiteiQ9JMJ4.

Expressioni

Gene expression databases

GenevisibleiQ9JMJ4. RN.

Interactioni

Subunit structurei

Homotetramer. Component of the Prp19 complex/PRP19C/Nineteen complex/NTC and related complexes described as PRP19-CDC5L splicing complex and PSO4 complex. A homotetramer of PRPF19, CDC5L, PLRG1 and BCAS2 constitute the core of those complexes. The interaction with CDC5L, PLRG1 and BCAS2 is direct within this core complex. At least three less stably associated proteins CTNNBL1, CWC15 and HSPA8 are found in the Prp19 complex. The Prp19 complex associates with the spliceosome during its assembly and remodeling recruiting additional proteins. Component of the XAB2 complex, a multimeric protein complex composed of XAB2, PRPF19, AQR, ZNF830, ISY1, and PPIE. Interacts with CWC22 and EIF4A3 in an RNA-independent manner. Interacts with RPA1 and RPA2; the PRP19-CDC5L complex is recruited to the sites of DNA repair where it interacts with the replication protein A complex (RPA). Interacts with SETMAR; required for SETMAR recruitment to site of DNA damage. Interacts with U2AF2; the interaction is direct and recruits the Prp19 complex to RNA polymerase II C-terminal domain (CTD) and the pre-mRNA. Interacts with PRPF3. Interacts with APEX1, DNTT and PSMB4. Interacts with KNSTRN (By similarity). Interacts with PSMC5 (By similarity). Interacts (via N-terminus) with CDC5L (PubMed:16352598).By similarity1 Publication

Protein-protein interaction databases

IntActiQ9JMJ4. 1 interaction.
STRINGi10116.ENSRNOP00000028373.

Structurei

3D structure databases

ProteinModelPortaliQ9JMJ4.
SMRiQ9JMJ4. Positions 3-55, 167-504.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 7372U-boxAdd
BLAST
Repeati219 – 25941WD 1Add
BLAST
Repeati262 – 30140WD 2Add
BLAST
Repeati304 – 34542WD 3Add
BLAST
Repeati348 – 38740WD 4Add
BLAST
Repeati390 – 42940WD 5Add
BLAST
Repeati433 – 47240WD 6Add
BLAST
Repeati473 – 50331WD 7Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni68 – 223156May mediate interaction with PSMC5By similarityAdd
BLAST

Domaini

The 7 WD repeats are necessary and sufficient to support interaction with the RPA complex.By similarity

Sequence similaritiesi

Belongs to the WD repeat PRP19 family.Curated
Contains 1 U-box domain.Curated
Contains 7 WD repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0289. Eukaryota.
ENOG410XPQV. LUCA.
GeneTreeiENSGT00840000129797.
HOGENOMiHOG000177308.
HOVERGENiHBG053697.
InParanoidiQ9JMJ4.
KOiK10599.
OMAiVYICKQW.
OrthoDBiEOG7K9K2R.
PhylomeDBiQ9JMJ4.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR013915. Pre-mRNA_splic_Prp19.
IPR000772. Ricin_B_lectin.
IPR003613. Ubox_domain.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF08606. Prp19. 1 hit.
PF04564. U-box. 1 hit.
PF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00504. Ubox. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS51698. U_BOX. 1 hit.
PS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 4 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9JMJ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLICSISNE VPEHPCVSPV SNHVYERRLI EKYIAENGTD PINNQPLSEE
60 70 80 90 100
QLIDIKVAHP IRPKPPSATS IPAILKALQD EWDAVMLHSF TLRQQLQTTR
110 120 130 140 150
QELSHALYQH DAACRVIARL TKEVTAAREA LATLKPQAGL IVPQAVPSSQ
160 170 180 190 200
PSVVGAGEPM DLGELVGMTP EIIQKLQDKA TVLTTERKKR GKTVPEELVK
210 220 230 240 250
PEELSKYRQV ASHVGLHSAS IPGILALDLC PSDTNKILTG GADKNVVVFD
260 270 280 290 300
KSTEQILATL KGHTKKVTSV VFHPSQELVF SASPDATIRI WSVPNTSCVQ
310 320 330 340 350
VVRAHESAVT GLSLHATGDY LLSSSDDQYW AFSDIQTGRV LTKVTDETSG
360 370 380 390 400
CSLTCAQFHP DGLIFGTGTM DSQIKIWDLK ERTNVANFPG HSGPITSIAF
410 420 430 440 450
SENGYYLATA ADDSSVKLWD LRKLKNFKTL QLDNNFEVKS LIFDQSGTYL
460 470 480 490 500
ALGGTDVQIY ICKQWTEILH FTEHSGLTTG VAFGHHAKFI ASTGMDRSLK

FYSL
Length:504
Mass (Da):55,239
Last modified:December 20, 2005 - v2
Checksum:iB2918188A0651024
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB020022 mRNA. Translation: BAA95215.2.
BC107669 mRNA. Translation: AAI07670.1.
RefSeqiNP_647549.2. NM_139333.3.
UniGeneiRn.19573.

Genome annotation databases

EnsembliENSRNOT00000028373; ENSRNOP00000028373; ENSRNOG00000020897.
GeneIDi246216.
KEGGirno:246216.
UCSCiRGD:708496. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB020022 mRNA. Translation: BAA95215.2.
BC107669 mRNA. Translation: AAI07670.1.
RefSeqiNP_647549.2. NM_139333.3.
UniGeneiRn.19573.

3D structure databases

ProteinModelPortaliQ9JMJ4.
SMRiQ9JMJ4. Positions 3-55, 167-504.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9JMJ4. 1 interaction.
STRINGi10116.ENSRNOP00000028373.

PTM databases

iPTMnetiQ9JMJ4.
PhosphoSiteiQ9JMJ4.

Proteomic databases

PaxDbiQ9JMJ4.
PeptideAtlasiQ9JMJ4.
PRIDEiQ9JMJ4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000028373; ENSRNOP00000028373; ENSRNOG00000020897.
GeneIDi246216.
KEGGirno:246216.
UCSCiRGD:708496. rat.

Organism-specific databases

CTDi27339.
RGDi708496. Prpf19.

Phylogenomic databases

eggNOGiKOG0289. Eukaryota.
ENOG410XPQV. LUCA.
GeneTreeiENSGT00840000129797.
HOGENOMiHOG000177308.
HOVERGENiHBG053697.
InParanoidiQ9JMJ4.
KOiK10599.
OMAiVYICKQW.
OrthoDBiEOG7K9K2R.
PhylomeDBiQ9JMJ4.

Enzyme and pathway databases

UniPathwayiUPA00143.
ReactomeiR-RNO-6781823. Formation of TC-NER Pre-Incision Complex.
R-RNO-6782135. Dual incision in TC-NER.
R-RNO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-RNO-72163. mRNA Splicing - Major Pathway.

Miscellaneous databases

PROiQ9JMJ4.

Gene expression databases

GenevisibleiQ9JMJ4. RN.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR020472. G-protein_beta_WD-40_rep.
IPR013915. Pre-mRNA_splic_Prp19.
IPR000772. Ricin_B_lectin.
IPR003613. Ubox_domain.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF08606. Prp19. 1 hit.
PF04564. U-box. 1 hit.
PF00400. WD40. 5 hits.
[Graphical view]
PRINTSiPR00320. GPROTEINBRPT.
SMARTiSM00504. Ubox. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]
SUPFAMiSSF50978. SSF50978. 1 hit.
PROSITEiPS51698. U_BOX. 1 hit.
PS00678. WD_REPEATS_1. 1 hit.
PS50082. WD_REPEATS_2. 4 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Involvement of the mouse Prp19 gene in neuronal/astroglial cell fate decisions."
    Urano Y., Iiduka M., Sugiyama A., Akiyama H., Uzawa K., Matsumoto G., Kawasaki Y., Tashiro F.
    J. Biol. Chem. 281:7498-7514(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH CDC5L, SUBCELLULAR LOCATION.
  2. "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.

Entry informationi

Entry nameiPRP19_RAT
AccessioniPrimary (citable) accession number: Q9JMJ4
Secondary accession number(s): Q3B7C6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: December 20, 2005
Last modified: July 6, 2016
This is version 118 of the entry and version 2 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.