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Protein

Pre-mRNA-processing factor 19

Gene

PRPF19

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 (PubMed:20595234). Recruited to RNA polymerase II C-terminal domain (CTD) and the pre-mRNA, it may also couple the transcriptional and spliceosomal machineries (PubMed:21536736). The XAB2 complex, which contains PRPF19, is also involved in pre-mRNA splicing, transcription and transcription-coupled repair (PubMed:17981804). 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 (PubMed:24332808). May also play a role in DNA double-strand break (DSB) repair by recruiting the repair factor SETMAR to altered DNA (PubMed:18263876). As part of the PSO4 complex may also be involved in the DNA interstrand cross-links/ICLs repair process (PubMed:16223718). In addition, may also mediate 'Lys-48'-linked polyubiquitination of substrates and play a role in proteasomal degradation (PubMed:11435423). 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 (By similarity).2 PublicationsBy similarity11 Publications

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.1 Publication

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.1 Publication
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

GO - Molecular functioni

  • identical protein binding Source: BHF-UCL
  • ubiquitin protein ligase activity Source: MGI
  • ubiquitin-protein transferase activity Source: GO_Central
  • ubiquitin-ubiquitin ligase activity Source: MGI

GO - Biological processi

Keywordsi

Molecular functionTransferase
Biological processDNA damage, DNA repair, mRNA processing, mRNA splicing, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiR-HSA-6781823 Formation of TC-NER Pre-Incision Complex
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-6782135 Dual incision in TC-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-72163 mRNA Splicing - Major Pathway
SignaLinkiQ9UMS4
UniPathwayi
UPA00143

Protein family/group databases

MoonDBiQ9UMS4 Predicted

Names & Taxonomyi

Protein namesi
Recommended name:
Pre-mRNA-processing factor 19Curated (EC:2.3.2.271 Publication)
Alternative name(s):
Nuclear matrix protein 2001 Publication
PRP19/PSO4 homolog1 Publication
Short name:
hPso41 Publication
RING-type E3 ubiquitin transferase PRP19Curated
Senescence evasion factor1 Publication
Gene namesi
Name:PRPF19Imported
Synonyms:NMP2001 Publication, PRP191 Publication, SNEV1 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000110107.8
HGNCiHGNC:17896 PRPF19
MIMi608330 gene
neXtProtiNX_Q9UMS4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Lipid droplet, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi405Y → A: Loss of interaction with the RPA complex and loss of recruitment to sites of DNA damage. 1 Publication1

Organism-specific databases

DisGeNETi27339
OpenTargetsiENSG00000110107
PharmGKBiPA134941355

Polymorphism and mutation databases

BioMutaiPRPF19
DMDMi55976619

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources2 Publications
ChainiPRO_00000511452 – 504Pre-mRNA-processing factor 19Add BLAST503

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources2 Publications1
Modified residuei122N6-acetyllysineCombined sources1
Modified residuei179N6-acetyllysineBy similarity1
Modified residuei244N6-acetyllysineBy similarity1
Modified residuei261N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9UMS4
MaxQBiQ9UMS4
PaxDbiQ9UMS4
PeptideAtlasiQ9UMS4
PRIDEiQ9UMS4
ProteomicsDBi85207

2D gel databases

REPRODUCTION-2DPAGEiIPI00004968
SWISS-2DPAGEiQ9UMS4

PTM databases

iPTMnetiQ9UMS4
PhosphoSitePlusiQ9UMS4
SwissPalmiQ9UMS4

Expressioni

Tissue specificityi

Ubiquitous. Weakly expressed in senescent cells of different tissue origins. Highly expressed in tumor cell lines.5 Publications

Inductioni

By gamma irradiation and chemical mutagens but not by UV irradiation.1 Publication

Gene expression databases

BgeeiENSG00000110107 Expressed in 228 organ(s), highest expression level in frontal cortex
CleanExiHS_PRPF19
ExpressionAtlasiQ9UMS4 baseline and differential
GenevisibleiQ9UMS4 HS

Organism-specific databases

HPAiCAB012448
HPA038051
HPA059070

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 PSMC5 (By similarity). Interacts with KNSTRN (PubMed:24718257). Interacts (via N-terminus) with CDC5L (By similarity). Interacts with KHDC4 (PubMed:19641227).By similarity15 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi118151, 195 interactors
CORUMiQ9UMS4
DIPiDIP-32978N
IntActiQ9UMS4, 50 interactors
MINTiQ9UMS4
STRINGi9606.ENSP00000227524

Structurei

Secondary structure

1504
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9UMS4
SMRiQ9UMS4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 73U-boxAdd BLAST72
Repeati219 – 259WD 1Add BLAST41
Repeati262 – 301WD 2Add BLAST40
Repeati304 – 345WD 3Add BLAST42
Repeati348 – 387WD 4Add BLAST40
Repeati390 – 429WD 5Add BLAST40
Repeati433 – 472WD 6Add BLAST40
Repeati473 – 503WD 7Add BLAST31

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni68 – 223May mediate interaction with PSMC5By similarityAdd BLAST156

Domaini

The 7 WD repeats are necessary and sufficient to support interaction with the RPA complex.1 Publication

Sequence similaritiesi

Belongs to the WD repeat PRP19 family.Curated

Keywords - Domaini

Repeat, WD repeat

Phylogenomic databases

eggNOGiKOG0289 Eukaryota
ENOG410XPQV LUCA
GeneTreeiENSGT00900000140925
HOGENOMiHOG000177308
HOVERGENiHBG053697
InParanoidiQ9UMS4
KOiK10599
OMAiKPQAGIV
OrthoDBiEOG091G05AH
PhylomeDBiQ9UMS4
TreeFamiTF105919

Family and domain databases

Gene3Di2.130.10.10, 1 hit
3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR013915 Pre-mRNA_splic_Prp19
IPR038959 Prp19
IPR000772 Ricin_B_lectin
IPR003613 Ubox_domain
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
IPR013083 Znf_RING/FYVE/PHD
PANTHERiPTHR43995 PTHR43995, 1 hit
PfamiView protein in Pfam
PF08606 Prp19, 1 hit
PF04564 U-box, 1 hit
PF00400 WD40, 5 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00504 Ubox, 1 hit
SM00320 WD40, 7 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS51698 U_BOX, 1 hit
PS00678 WD_REPEATS_1, 1 hit
PS50082 WD_REPEATS_2, 4 hits
PS50294 WD_REPEATS_REGION, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 4 potential isoforms that are computationally mapped.Show allAlign All

Q9UMS4-1 [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
KSSEQILATL KGHTKKVTSV VFHPSQDLVF SASPDATIRI WSVPNASCVQ
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):55,181
Last modified:May 1, 2000 - v1
Checksum:iB34C37496E8AA032
GO

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0YGZ5H0YGZ5_HUMAN
Pre-mRNA-processing factor 19
PRPF19
119Annotation score:
F5GY56F5GY56_HUMAN
Pre-mRNA-processing factor 19
PRPF19
252Annotation score:
F5H2I0F5H2I0_HUMAN
Pre-mRNA-processing factor 19
PRPF19
104Annotation score:
H0YGF3H0YGF3_HUMAN
Pre-mRNA-processing factor 19
PRPF19
45Annotation score:

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131186 mRNA Translation: CAB51857.1
BC008719 mRNA Translation: AAH08719.1
BC018665 mRNA Translation: AAH18665.1
BC018698 mRNA Translation: AAH18698.1
CCDSiCCDS7995.1
RefSeqiNP_055317.1, NM_014502.4
UniGeneiHs.502705

Genome annotation databases

EnsembliENST00000227524; ENSP00000227524; ENSG00000110107
GeneIDi27339
KEGGihsa:27339
UCSCiuc001nqf.4 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ131186 mRNA Translation: CAB51857.1
BC008719 mRNA Translation: AAH08719.1
BC018665 mRNA Translation: AAH18665.1
BC018698 mRNA Translation: AAH18698.1
CCDSiCCDS7995.1
RefSeqiNP_055317.1, NM_014502.4
UniGeneiHs.502705

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LG8X-ray1.89A169-504[»]
5MQFelectron microscopy5.90G/H/I/J1-504[»]
5XJCelectron microscopy3.60q/r/s/t1-504[»]
5YZGelectron microscopy4.10q/r/s/t1-504[»]
5Z56electron microscopy5.10q/r/s/t1-504[»]
5Z57electron microscopy6.50q/r/s/t1-504[»]
ProteinModelPortaliQ9UMS4
SMRiQ9UMS4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi118151, 195 interactors
CORUMiQ9UMS4
DIPiDIP-32978N
IntActiQ9UMS4, 50 interactors
MINTiQ9UMS4
STRINGi9606.ENSP00000227524

Protein family/group databases

MoonDBiQ9UMS4 Predicted

PTM databases

iPTMnetiQ9UMS4
PhosphoSitePlusiQ9UMS4
SwissPalmiQ9UMS4

Polymorphism and mutation databases

BioMutaiPRPF19
DMDMi55976619

2D gel databases

REPRODUCTION-2DPAGEiIPI00004968
SWISS-2DPAGEiQ9UMS4

Proteomic databases

EPDiQ9UMS4
MaxQBiQ9UMS4
PaxDbiQ9UMS4
PeptideAtlasiQ9UMS4
PRIDEiQ9UMS4
ProteomicsDBi85207

Protocols and materials databases

DNASUi27339
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000227524; ENSP00000227524; ENSG00000110107
GeneIDi27339
KEGGihsa:27339
UCSCiuc001nqf.4 human

Organism-specific databases

CTDi27339
DisGeNETi27339
EuPathDBiHostDB:ENSG00000110107.8
GeneCardsiPRPF19
HGNCiHGNC:17896 PRPF19
HPAiCAB012448
HPA038051
HPA059070
MIMi608330 gene
neXtProtiNX_Q9UMS4
OpenTargetsiENSG00000110107
PharmGKBiPA134941355
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0289 Eukaryota
ENOG410XPQV LUCA
GeneTreeiENSGT00900000140925
HOGENOMiHOG000177308
HOVERGENiHBG053697
InParanoidiQ9UMS4
KOiK10599
OMAiKPQAGIV
OrthoDBiEOG091G05AH
PhylomeDBiQ9UMS4
TreeFamiTF105919

Enzyme and pathway databases

UniPathwayi
UPA00143

ReactomeiR-HSA-6781823 Formation of TC-NER Pre-Incision Complex
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-6782135 Dual incision in TC-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-72163 mRNA Splicing - Major Pathway
SignaLinkiQ9UMS4

Miscellaneous databases

ChiTaRSiPRPF19 human
GeneWikiiPRPF19
GenomeRNAii27339
PROiPR:Q9UMS4
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000110107 Expressed in 228 organ(s), highest expression level in frontal cortex
CleanExiHS_PRPF19
ExpressionAtlasiQ9UMS4 baseline and differential
GenevisibleiQ9UMS4 HS

Family and domain databases

Gene3Di2.130.10.10, 1 hit
3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR020472 G-protein_beta_WD-40_rep
IPR013915 Pre-mRNA_splic_Prp19
IPR038959 Prp19
IPR000772 Ricin_B_lectin
IPR003613 Ubox_domain
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR019775 WD40_repeat_CS
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
IPR013083 Znf_RING/FYVE/PHD
PANTHERiPTHR43995 PTHR43995, 1 hit
PfamiView protein in Pfam
PF08606 Prp19, 1 hit
PF04564 U-box, 1 hit
PF00400 WD40, 5 hits
PRINTSiPR00320 GPROTEINBRPT
SMARTiView protein in SMART
SM00504 Ubox, 1 hit
SM00320 WD40, 7 hits
SUPFAMiSSF50978 SSF50978, 1 hit
PROSITEiView protein in PROSITE
PS51698 U_BOX, 1 hit
PS00678 WD_REPEATS_1, 1 hit
PS50082 WD_REPEATS_2, 4 hits
PS50294 WD_REPEATS_REGION, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPRP19_HUMAN
AccessioniPrimary (citable) accession number: Q9UMS4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: May 1, 2000
Last modified: November 7, 2018
This is version 172 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
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