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Protein

Cleavage and polyadenylation specificity factor subunit 5

Gene

Nudt21

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Component of the cleavage factor Im (CFIm) complex that plays a key role in pre-mRNA 3'-processing. Involved in association with CPSF6 or CPSF7 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. NUDT21/CPSF5 binds to cleavage and polyadenylation RNA substrates. The homodimer mediates simultaneous sequence-specific recognition of two 5'-UGUA-3' elements within the pre-mRNA. Binds to, but does not hydrolyze mono- and di-adenosine nucleotides. May have a role in mRNA export (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

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 5
Alternative name(s):
Nucleoside diphosphate-linked moiety X motif 21
Short name:
Nudix motif 21
Gene namesi
Name:Nudt21
Synonyms:Cpsf5
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 19

Organism-specific databases

RGDi1305766. Nudt21.

Subcellular locationi

  • Nucleus By similarity

  • Note: In punctate subnuclear structures localized adjacent to nuclear speckles, called paraspeckles.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 227226Cleavage and polyadenylation specificity factor subunit 5PRO_0000057153Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei23 – 231N6-acetyllysineBy similarity
Modified residuei29 – 291N6-acetyllysineBy similarity
Modified residuei40 – 401PhosphotyrosineBy similarity
Modified residuei56 – 561N6-acetyllysineBy similarity

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).By similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiQ4KM65.
PRIDEiQ4KM65.

PTM databases

iPTMnetiQ4KM65.
PhosphoSiteiQ4KM65.

Expressioni

Gene expression databases

ExpressionAtlasiQ4KM65. baseline and differential.
GenevisibleiQ4KM65. RN.

Interactioni

Subunit structurei

Homodimer. Component of the cleavage factor Im (CFIm) complex, composed of, at least, NUDT21/CPSF5 and CPSF6 or CPSF7. Within the cleavage factor Im complex, the NUDT21/CPSF5 homodimer is at the core of a heterotetramer, and is clasped by two additional subunits (CPSF6 or CPSF7). Interacts with CPSF6, CPSF7, PABPN1 and SNRNP70. Interacts with PAPOLA; the interaction is diminished by acetylation (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei55 – 551Interaction with RNABy similarity
Sitei63 – 631Interaction with RNABy similarity
Sitei208 – 2081Interaction with RNABy similarity

Protein-protein interaction databases

BioGridi253672. 2 interactions.
STRINGi10116.ENSRNOP00000026297.

Structurei

3D structure databases

ProteinModelPortaliQ4KM65.
SMRiQ4KM65. Positions 22-227.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini76 – 201126Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni2 – 147146Necessary for RNA-bindingBy similarityAdd
BLAST
Regioni81 – 16080Necessary for interactions with PAPOLA and PABPN1By similarityAdd
BLAST
Regioni102 – 1043Interaction with RNABy similarity

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi109 – 13022Nudix boxAdd
BLAST

Sequence similaritiesi

Belongs to the Nudix hydrolase family. CPSF5 subfamily.Curated
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1689. Eukaryota.
ENOG410XS8Z. LUCA.
GeneTreeiENSGT00390000015814.
HOGENOMiHOG000161320.
HOVERGENiHBG052968.
InParanoidiQ4KM65.
KOiK14397.
OMAiGDCLAQW.
OrthoDBiEOG7KSX9M.
PhylomeDBiQ4KM65.
TreeFamiTF106356.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR016706. Cleav_polyA_spec_factor_su5.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR13047. PTHR13047. 1 hit.
PfamiPF13869. NUDIX_2. 1 hit.
[Graphical view]
PIRSFiPIRSF017888. CPSF-25. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

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.

Cross-referencesi

Sequence databases

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

3D structure databases

ProteinModelPortaliQ4KM65.
SMRiQ4KM65. Positions 22-227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi253672. 2 interactions.
STRINGi10116.ENSRNOP00000026297.

PTM databases

iPTMnetiQ4KM65.
PhosphoSiteiQ4KM65.

Proteomic databases

PaxDbiQ4KM65.
PRIDEiQ4KM65.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi11051.
RGDi1305766. Nudt21.

Phylogenomic databases

eggNOGiKOG1689. Eukaryota.
ENOG410XS8Z. LUCA.
GeneTreeiENSGT00390000015814.
HOGENOMiHOG000161320.
HOVERGENiHBG052968.
InParanoidiQ4KM65.
KOiK14397.
OMAiGDCLAQW.
OrthoDBiEOG7KSX9M.
PhylomeDBiQ4KM65.
TreeFamiTF106356.

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.

Miscellaneous databases

NextBioi633328.
PROiQ4KM65.

Gene expression databases

ExpressionAtlasiQ4KM65. baseline and differential.
GenevisibleiQ4KM65. RN.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR016706. Cleav_polyA_spec_factor_su5.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PANTHERiPTHR13047. PTHR13047. 1 hit.
PfamiPF13869. NUDIX_2. 1 hit.
[Graphical view]
PIRSFiPIRSF017888. CPSF-25. 1 hit.
SUPFAMiSSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "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: Spleen.

Entry informationi

Entry nameiCPSF5_RAT
AccessioniPrimary (citable) accession number: Q4KM65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: August 2, 2005
Last modified: January 20, 2016
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.