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Protein

Cleavage and polyadenylation specificity factor subunit 3

Gene

Cpsf3

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

Functioni

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. Has endonuclease activity, and functions as mRNA 3'-end-processing endonuclease. Also involved in the histone 3'-end pre-mRNA processing. U7 snRNP-dependent protein that induces both the 3' endoribonucleolytic cleavage of histone pre-mRNAs and acts as a 5' to 3' exonuclease for degrading the subsequent downstream cleavage product (DCP) of mature histone mRNAs. Cleavage occurs after the 5'-ACCCA-3' sequence in the histone pre-mRNA leaving a 3'hydroxyl group on the upstream fragment containing the stem loop (SL) and 5' phosphate on the downstream cleavage product (DCP) starting with CU nucleotides. The U7-dependent 5' to 3' exonuclease activity is processive and degrades the DCP RNA substrate even after complete removal of the U7-binding site. Binds to the downstream cleavage product (DCP) of histone pre-mRNAs and the cleaved DCP RNA substrate in a U7 snRNP dependent manner.3 Publications

Cofactori

Zn2+By similarityNote: Binds 2 Zn2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi71 – 711Zinc 1By similarity
Metal bindingi73 – 731Zinc 1By similarity
Metal bindingi75 – 751Zinc 2By similarity
Metal bindingi76 – 761Zinc 2By similarity
Metal bindingi158 – 1581Zinc 1By similarity
Metal bindingi179 – 1791Zinc 1By similarity
Metal bindingi179 – 1791Zinc 2By similarity
Active sitei396 – 3961Proton donorSequence analysis
Metal bindingi418 – 4181Zinc 2By similarity

GO - Molecular functioni

  • 5'-3' exonuclease activity Source: UniProtKB
  • endoribonuclease activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • RNA binding Source: UniProtKB

GO - Biological processi

  • mRNA 3'-end processing by stem-loop binding and cleavage Source: UniProtKB
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
  • RNA phosphodiester bond hydrolysis, endonucleolytic Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Ribonucleoprotein

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72187. mRNA 3'-end processing.
R-MMU-77595. Processing of Intronless Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 3 (EC:3.1.27.-)
Alternative name(s):
Cleavage and polyadenylation specificity factor 73 kDa subunit
Short name:
CPSF 73 kDa subunit
Short name:
mRNA 3'-end-processing endonuclease CPSF-73
Gene namesi
Name:Cpsf3
Synonyms:Cpsf73
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 12

Organism-specific databases

MGIiMGI:1859328. Cpsf3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 684683Cleavage and polyadenylation specificity factor subunit 3PRO_0000074401Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Cross-linki462 – 462Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki465 – 465Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Cross-linki545 – 545Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Modified residuei659 – 6591PhosphoserineCombined sources
Modified residuei681 – 6811PhosphothreonineBy similarity

Post-translational modificationi

Sumoylated on Lys-462, Lys-465 and Lys-545, preferentially by SUMO3.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ9QXK7.
MaxQBiQ9QXK7.
PaxDbiQ9QXK7.
PRIDEiQ9QXK7.

PTM databases

iPTMnetiQ9QXK7.
PhosphoSiteiQ9QXK7.

Expressioni

Gene expression databases

BgeeiQ9QXK7.
CleanExiMM_CPSF3.
GenevisibleiQ9QXK7. MM.

Interactioni

Subunit structurei

Component of the cleavage and polyadenylation specificity factor (CPSF) complex, composed of CPSF1, CPSF2, CPSF3, CPSF4 and FIP1L1. Interacts with CPSF2, CSTF2 and SYMPK. Interacts with TUT1; the interaction is direct and mediates the recruitment of the CPSF complex on the 3'UTR of pre-mRNAs. Interacts with WDR33 (By similarity). Interacts with ZC3H3 (PubMed:16115198).By similarity1 Publication

Protein-protein interaction databases

BioGridi207665. 1 interaction.
IntActiQ9QXK7. 1 interaction.
MINTiMINT-4091960.
STRINGi10090.ENSMUSP00000068148.

Structurei

3D structure databases

ProteinModelPortaliQ9QXK7.
SMRiQ9QXK7. Positions 7-459.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1137. Eukaryota.
COG1236. LUCA.
GeneTreeiENSGT00840000129795.
HOGENOMiHOG000203394.
HOVERGENiHBG051107.
InParanoidiQ9QXK7.
KOiK14403.
OMAiEISFSAH.
OrthoDBiEOG7BW0HT.
TreeFamiTF105643.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR022712. Beta_Casp.
IPR021718. CPSF73-100_C.
IPR001279. Metallo-B-lactamas.
IPR011108. RMMBL.
[Graphical view]
PfamiPF10996. Beta-Casp. 1 hit.
PF11718. CPSF73-100_C. 1 hit.
PF00753. Lactamase_B. 1 hit.
PF07521. RMMBL. 1 hit.
[Graphical view]
SMARTiSM01027. Beta-Casp. 1 hit.
SM01098. CPSF73-100_C. 1 hit.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9QXK7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAIPAEESD QLLIRPLGAG QEVGRSCIIL EFKGRKIMLD CGIHPGLEGM
60 70 80 90 100
DALPYIDLID PAEIDLLLIS HFHLDHCGAL PWFLQKTSFK GRTFMTHATK
110 120 130 140 150
AIYRWLLSDY VKVSNISADD MLYTETDLEE SMDKIETINF HEVKEVAGIK
160 170 180 190 200
FWCYHAGHVL GAAMFMIEIA GVKLLYTGDF SRQEDRHLMA AEIPNIKPDI
210 220 230 240 250
LIIESTYGTH IHEKREEREA RFCNTVHDIV NRGGRGLIPV FALGRAQELL
260 270 280 290 300
LILDEYWQNH PELHDIPIYY ASSLAKKCMA VYQTYVNAMN DKIRKQININ
310 320 330 340 350
NPFVFKHISN LKSMDHFDDI GPSVVMASPG MIQNGLSREL FESWCTDKRN
360 370 380 390 400
GVIIAGYCVE GTLAKHIMSE PEEITTMSGQ KLPLKMSVDY ISFSAHTDYQ
410 420 430 440 450
QTSEFIRALK PPHVILVHGE QNEMARLKAA LIREYEDNDE VHIEVHNPRN
460 470 480 490 500
TEAVTLNFRG EKLAKVMGFL ADKKPEQGQR VSGILVKRNF NYHILSPCDL
510 520 530 540 550
SNYTDLAMST VKQTQAIPYT GPFYLLYYQL QKLTGDVEEL EIQEKPALKV
560 570 580 590 600
FKSITVVQEP GMVVLEWLAN PSNDMYADTV TTVILEVQSN PKIRKGAVQK
610 620 630 640 650
VSKKLEMHVY SKRLEVMLQD IFGEDCVSVK DDSVLSVTVD GKTANINLET
660 670 680
RAVECEEGSE DDESLREMVE LAAQRLYEAL TPVH
Length:684
Mass (Da):77,505
Last modified:July 27, 2011 - v2
Checksum:i043D09F54284B423
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti223 – 2242CN → WH in AAF19420 (Ref. 1) Curated
Sequence conflicti541 – 5411E → D in AAF19420 (Ref. 1) Curated
Sequence conflicti564 – 5652VL → GS in AAF19420 (Ref. 1) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF203969 mRNA. Translation: AAF19420.1.
BC023297 mRNA. Translation: AAH23297.1.
CCDSiCCDS25834.1.
RefSeqiNP_061283.2. NM_018813.3.
UniGeneiMm.356778.

Genome annotation databases

EnsembliENSMUST00000067284; ENSMUSP00000068148; ENSMUSG00000054309.
GeneIDi54451.
KEGGimmu:54451.
UCSCiuc007ndp.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF203969 mRNA. Translation: AAF19420.1.
BC023297 mRNA. Translation: AAH23297.1.
CCDSiCCDS25834.1.
RefSeqiNP_061283.2. NM_018813.3.
UniGeneiMm.356778.

3D structure databases

ProteinModelPortaliQ9QXK7.
SMRiQ9QXK7. Positions 7-459.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi207665. 1 interaction.
IntActiQ9QXK7. 1 interaction.
MINTiMINT-4091960.
STRINGi10090.ENSMUSP00000068148.

PTM databases

iPTMnetiQ9QXK7.
PhosphoSiteiQ9QXK7.

Proteomic databases

EPDiQ9QXK7.
MaxQBiQ9QXK7.
PaxDbiQ9QXK7.
PRIDEiQ9QXK7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000067284; ENSMUSP00000068148; ENSMUSG00000054309.
GeneIDi54451.
KEGGimmu:54451.
UCSCiuc007ndp.2. mouse.

Organism-specific databases

CTDi51692.
MGIiMGI:1859328. Cpsf3.

Phylogenomic databases

eggNOGiKOG1137. Eukaryota.
COG1236. LUCA.
GeneTreeiENSGT00840000129795.
HOGENOMiHOG000203394.
HOVERGENiHBG051107.
InParanoidiQ9QXK7.
KOiK14403.
OMAiEISFSAH.
OrthoDBiEOG7BW0HT.
TreeFamiTF105643.

Enzyme and pathway databases

ReactomeiR-MMU-109688. Cleavage of Growing Transcript in the Termination Region.
R-MMU-72163. mRNA Splicing - Major Pathway.
R-MMU-72187. mRNA 3'-end processing.
R-MMU-77595. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

ChiTaRSiCpsf3. mouse.
NextBioi311332.
PROiQ9QXK7.
SOURCEiSearch...

Gene expression databases

BgeeiQ9QXK7.
CleanExiMM_CPSF3.
GenevisibleiQ9QXK7. MM.

Family and domain databases

Gene3Di3.60.15.10. 1 hit.
InterProiIPR022712. Beta_Casp.
IPR021718. CPSF73-100_C.
IPR001279. Metallo-B-lactamas.
IPR011108. RMMBL.
[Graphical view]
PfamiPF10996. Beta-Casp. 1 hit.
PF11718. CPSF73-100_C. 1 hit.
PF00753. Lactamase_B. 1 hit.
PF07521. RMMBL. 1 hit.
[Graphical view]
SMARTiSM01027. Beta-Casp. 1 hit.
SM01098. CPSF73-100_C. 1 hit.
SM00849. Lactamase_B. 1 hit.
[Graphical view]
SUPFAMiSSF56281. SSF56281. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Wang H., Chen W., Yu S., Xie L.
    Submitted (NOV-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/cJ.
  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].
    Strain: FVB/N.
    Tissue: Salivary gland.
  3. "The polyadenylation factor CPSF-73 is involved in histone-pre-mRNA processing."
    Dominski Z., Yang X.-C., Marzluff W.F.
    Cell 123:37-48(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING.
  4. "Smicl is a novel Smad interacting protein and cleavage and polyadenylation specificity factor associated protein."
    Collart C., Remacle J.E., Barabino S., van Grunsven L.A., Nelles L., Schellens A., Van de Putte T., Pype S., Huylebroeck D., Verschueren K.
    Genes Cells 10:897-906(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ZC3H3.
  5. "Studies of the 5' exonuclease and endonuclease activities of CPSF-73 in histone pre-mRNA processing."
    Yang X.-C., Sullivan K.D., Marzluff W.F., Dominski Z.
    Mol. Cell. Biol. 29:31-42(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING.
  6. "Three proteins of the U7-specific Sm ring function as the molecular ruler to determine the site of 3'-end processing in mammalian histone pre-mRNA."
    Yang X.-C., Torres M.P., Marzluff W.F., Dominski Z.
    Mol. Cell. Biol. 29:4045-4056(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RNA-BINDING.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-659, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brown adipose tissue, Liver, Lung, Spleen and Testis.

Entry informationi

Entry nameiCPSF3_MOUSE
AccessioniPrimary (citable) accession number: Q9QXK7
Secondary accession number(s): Q8CIM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: July 27, 2011
Last modified: May 11, 2016
This is version 108 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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  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.