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Protein

Cleavage and polyadenylation specificity factor subunit 5

Gene

Nudt21

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs. CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation. The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs. NUDT21/CPSF5 activates indirectly the mRNA 3'-processing machinery by recruiting CPSF6 and/or CPSF7. Binds to 5'-UGUA-3' elements localized upstream of pA signals that act as enhancers of pre-mRNA 3'-end processing. The homodimer mediates simultaneous sequence-specific recognition of two 5'-UGUA-3' elements within the pre-mRNA. Plays a role in somatic cell fate transitions and pluripotency by regulating widespread changes in gene expression through an APA-dependent function. Binds to chromatin. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides.By similarity

Caution

Lacks the conserved metal-binding residues in the NUDIX motif and is not expected to have hydrolase activity.Curated

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processDifferentiation, mRNA processing

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 5By similarity
Alternative name(s):
Nucleoside diphosphate-linked moiety X motif 21
Short name:
Nudix motif 21
Nudix hydrolase 21Curated
Gene namesi
Name:Nudt21Imported
Synonyms:Cpsf5By similarity
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 19

Organism-specific databases

RGDi1305766 Nudt21

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, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000571532 – 227Cleavage and polyadenylation specificity factor subunit 5Add BLAST226

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei15Omega-N-methylarginineBy similarity1
Modified residuei23N6-acetyllysineBy similarity1
Modified residuei29N6-acetyllysineBy similarity1
Modified residuei40PhosphotyrosineBy similarity1
Modified residuei56N6-acetyllysineBy similarity1

Post-translational modificationi

Acetylated mainly by p300/CBP, recruited to the complex by CPSF6. Acetylation decreases interaction with PAPAO. Deacetylated by the class I/II HDACs, HDAC1, HDAC3 and HDAC10, and by the class III HDACs, SIRT1 AND SIRT2.By similarity

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

PaxDbiQ4KM65
PRIDEiQ4KM65

PTM databases

iPTMnetiQ4KM65
PhosphoSitePlusiQ4KM65

Expressioni

Gene expression databases

BgeeiENSRNOG00000042983
ExpressionAtlasiQ4KM65 baseline and differential
GenevisibleiQ4KM65 RN

Interactioni

Subunit structurei

Homodimer (via N- and C-terminus); binds RNA as homodimer. Component of the cleavage factor Im (CFIm) complex which is an heterotetramer composed of two subunits of NUDT21/CPSF5 and two subunits of CPSF6 or CPSF7 or an heterodimer of CPSF6 and CPSF7. The cleavage factor Im (CFIm) complex associates with the CPSF and CSTF complexes to promote the assembly of the core mRNA 3'-processing machinery. Interacts with CPSF6 (via the RRM domain); this interaction is direct and enhances binding to RNA. Interacts with CPSF7. Interacts with FIP1L1; this interaction occurs in a RNA sequence-specific manner. Interacts with PABPN1. Interacts (via N-terminus) with PAPOLA (via C-terminus); this interaction is direct and diminished by acetylation. Interacts with SNRNP70.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei55Interaction with RNABy similarity1
Sitei63Interaction with RNABy similarity1

GO - Molecular functioni

Protein-protein interaction databases

BioGridi253672, 2 interactors
STRINGi10116.ENSRNOP00000026297

Structurei

3D structure databases

ProteinModelPortaliQ4KM65
SMRiQ4KM65
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini76 – 201Nudix hydrolasePROSITE-ProRule annotationAdd BLAST126

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 147Necessary for RNA-bindingBy similarityAdd BLAST146
Regioni81 – 160Necessary for interactions with PAPOLA and PABPN1By similarityAdd BLAST80
Regioni102 – 104Interaction with RNABy similarity3

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi109 – 130Nudix boxAdd BLAST22

Sequence similaritiesi

Belongs to the Nudix hydrolase family. CPSF5 subfamily.Curated

Phylogenomic databases

eggNOGiKOG1689 Eukaryota
ENOG410XS8Z LUCA
GeneTreeiENSGT00390000015814
HOGENOMiHOG000161320
HOVERGENiHBG052968
InParanoidiQ4KM65
KOiK14397
OMAiCLAQWWR
OrthoDBiEOG091G0HGL
PhylomeDBiQ4KM65
TreeFamiTF106356

Family and domain databases

InterProiView protein in InterPro
IPR016706 Cleav_polyA_spec_factor_su5
IPR015797 NUDIX_hydrolase-like_dom_sf
IPR000086 NUDIX_hydrolase_dom
PANTHERiPTHR13047 PTHR13047, 1 hit
PfamiView protein in Pfam
PF13869 NUDIX_2, 1 hit
PIRSFiPIRSF017888 CPSF-25, 1 hit
SUPFAMiSSF55811 SSF55811, 1 hit
PROSITEiView protein in PROSITE
PS51462 NUDIX, 1 hit

Sequencei

Sequence statusi: Complete.

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

Q4KM65-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVVPPNRSQ TGWPRGVNQF GNKYIQQTKP LTLERTINLY PLTNYTFGTK
60 70 80 90 100
EPLYEKDSSV AARFQRMREE FDKIGMRRTV EGVLIVHEHR LPHVLLLQLG
110 120 130 140 150
TTFFKLPGGE LNPGEDEVEG LKRLMTEILG RQDGVLQDWV IDDCIGNWWR
160 170 180 190 200
PNFEPPQYPY IPAHITKPKE HKKLFLVQLQ EKALFAVPKN YKLVAAPLFE
210 220
LYDNAPGYGP IISSLPQLLS RFNFIYN
Length:227
Mass (Da):26,240
Last modified:August 2, 2005 - v1
Checksum:i93AEF53557811DC5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC098748 mRNA Translation: AAH98748.1
RefSeqiNP_001034093.1, NM_001039004.1
UniGeneiRn.199052

Genome annotation databases

EnsembliENSRNOT00000026297; ENSRNOP00000026297; ENSRNOG00000042983
GeneIDi291877
KEGGirno:291877
UCSCiRGD:1305766 rat

Similar proteinsi

Entry informationi

Entry nameiCPSF5_RAT
AccessioniPrimary (citable) accession number: Q4KM65
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: August 2, 2005
Last modified: April 25, 2018
This is version 96 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health