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Protein

Cleavage and polyadenylation specificity factor subunit 5

Gene

NUDT21

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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.6 Publications

GO - Molecular functioni

  • AU-rich element binding Source: UniProtKB
  • histone deacetylase binding Source: UniProtKB
  • hydrolase activity Source: InterPro
  • mRNA binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

  • mRNA 3'-end processing Source: Reactome
  • mRNA polyadenylation Source: UniProtKB
  • mRNA processing Source: UniProtKB
  • mRNA splicing, via spliceosome Source: Reactome
  • protein tetramerization Source: UniProtKB
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000167005-MONOMER.
ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-77595. Processing of Intronless Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Cleavage and polyadenylation specificity factor subunit 5
Alternative name(s):
Cleavage and polyadenylation specificity factor 25 kDa subunit
Short name:
CFIm25
Short name:
CPSF 25 kDa subunit
Nucleoside diphosphate-linked moiety X motif 21
Short name:
Nudix motif 21
Pre-mRNA cleavage factor Im 25 kDa subunit
Gene namesi
Name:NUDT21
Synonyms:CFIM25, CPSF25, CPSF5
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:13870. NUDT21.

Subcellular locationi

GO - Cellular componenti

  • centrosome Source: LIFEdb
  • microtubule organizing center Source: HPA
  • mRNA cleavage factor complex Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • paraspeckles Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi23K → R: Abolishes acetylation. 1 Publication1
Mutagenesisi29K → R: No effect on acetylation. 1 Publication1
Mutagenesisi55E → A: Reduces affinity for UGUA RNA by 88%. 2 Publications1
Mutagenesisi63R → S: Reduces affinity for UGUA RNA by 99%. 2 Publications1
Mutagenesisi81E → A: Reduces affinity for UGUA RNA by 12%. 1 Publication1
Mutagenesisi103F → A: Reduces affinity for UGUA RNA by 99%. 2 Publications1
Mutagenesisi103F → W: Reduces affinity for UGUA RNA by over 90%. 2 Publications1
Mutagenesisi154E → A: Reduces affinity for UGUA RNA by 50%. 1
Mutagenesisi158Y → A: Abolishes interaction with CPSF6; when associated with A-160. 1 Publication1
Mutagenesisi160Y → A: Abolishes interaction with CPSF6; when associated with A-158. 1 Publication1

Organism-specific databases

DisGeNETi11051.
OpenTargetsiENSG00000167005.
PharmGKBiPA26845.

Polymorphism and mutation databases

BioMutaiNUDT21.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000571502 – 227Cleavage and polyadenylation specificity factor subunit 5Add BLAST226

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserine1 Publication1
Modified residuei15Omega-N-methylarginineCombined sources1
Modified residuei23N6-acetyllysineCombined sources1 Publication1
Modified residuei29N6-acetyllysineCombined sources1
Modified residuei40PhosphotyrosineCombined sources1
Modified residuei56N6-acetyllysineCombined sources1

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 SIRT2.2 Publications

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiO43809.
MaxQBiO43809.
PaxDbiO43809.
PeptideAtlasiO43809.
PRIDEiO43809.
TopDownProteomicsiO43809.

2D gel databases

UCD-2DPAGEO43809.

PTM databases

iPTMnetiO43809.
PhosphoSitePlusiO43809.
SwissPalmiO43809.

Expressioni

Gene expression databases

BgeeiENSG00000167005.
CleanExiHS_NUDT21.
ExpressionAtlasiO43809. baseline and differential.
GenevisibleiO43809. HS.

Organism-specific databases

HPAiHPA019863.
HPA074228.

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.11 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei55Interaction with RNA1
Sitei63Interaction with RNA1
Sitei208Interaction with RNA1

Binary interactionsi

WithEntry#Exp.IntActNotes
itself4EBI-355720,EBI-355720
ATXN1P542532EBI-355720,EBI-930964
CARM1Q86X552EBI-355720,EBI-2339854
CPSF6Q166305EBI-355720,EBI-358410
CPSF6Q16630-23EBI-355720,EBI-11088043
CPSF7Q8N6845EBI-355720,EBI-746909
GOLGA2Q083793EBI-355720,EBI-618309
MYL6P606603EBI-355720,EBI-300817
TRIM27P143735EBI-355720,EBI-719493

GO - Molecular functioni

  • histone deacetylase binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi116237. 121 interactors.
DIPiDIP-42502N.
IntActiO43809. 79 interactors.
MINTiMINT-5002263.
STRINGi9606.ENSP00000300291.

Structurei

Secondary structure

1227
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni31 – 33Combined sources3
Beta strandi36 – 39Combined sources4
Helixi42 – 44Combined sources3
Beta strandi45 – 50Combined sources6
Helixi60 – 74Combined sources15
Beta strandi76 – 88Combined sources13
Beta strandi91 – 100Combined sources10
Beta strandi103 – 105Combined sources3
Beta strandi107 – 110Combined sources4
Helixi117 – 129Combined sources13
Beta strandi132 – 134Combined sources3
Beta strandi140 – 150Combined sources11
Beta strandi152 – 155Combined sources4
Beta strandi158 – 160Combined sources3
Beta strandi169 – 178Combined sources10
Beta strandi181 – 188Combined sources8
Beta strandi192 – 197Combined sources6
Helixi198 – 201Combined sources4
Helixi205 – 212Combined sources8
Helixi215 – 219Combined sources5
Beta strandi223 – 226Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CL3X-ray1.90A21-227[»]
2J8QX-ray2.30A/B24-227[»]
3BAPX-ray1.85A1-227[»]
3BHOX-ray1.80A20-227[»]
3MDGX-ray2.22A/B1-227[»]
3MDIX-ray2.07A/B1-227[»]
3N9UX-ray1.92A/B21-227[»]
3P5TX-ray2.70A/B/C/D/E/F34-227[»]
3P6YX-ray2.90A/B/E/F/I/J/M/N34-227[»]
3Q2SX-ray2.90A/B21-227[»]
3Q2TX-ray3.06A/B21-227[»]
ProteinModelPortaliO43809.
SMRiO43809.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43809.

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-bindingAdd BLAST146
Regioni81 – 160Necessary for interactions with PAPOLA and PABPN1Add BLAST80
Regioni102 – 104Interaction with RNA3

Motif

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

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.
InParanoidiO43809.
KOiK14397.
OMAiGDCLAQW.
OrthoDBiEOG091G0HGL.
PhylomeDBiO43809.
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.

O43809-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVVPPNRSQ TGWPRGVTQF 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):26,227
Last modified:June 1, 1998 - v1
Checksum:iD204243E57F1CCC5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti57D → G in CAG33200 (Ref. 2) Curated1
Sequence conflicti112N → D in CAD97606 (PubMed:17974005).Curated1
Sequence conflicti218L → P in CAD97606 (PubMed:17974005).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ001810 mRNA. Translation: CAA05026.1.
CR456919 mRNA. Translation: CAG33200.1.
BX537360 mRNA. Translation: CAD97606.1.
AC092140 Genomic DNA. No translation available.
BC001403 mRNA. Translation: AAH01403.1.
CCDSiCCDS10760.1.
RefSeqiNP_008937.1. NM_007006.2.
UniGeneiHs.528834.

Genome annotation databases

EnsembliENST00000300291; ENSP00000300291; ENSG00000167005.
GeneIDi11051.
KEGGihsa:11051.
UCSCiuc002eja.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ001810 mRNA. Translation: CAA05026.1.
CR456919 mRNA. Translation: CAG33200.1.
BX537360 mRNA. Translation: CAD97606.1.
AC092140 Genomic DNA. No translation available.
BC001403 mRNA. Translation: AAH01403.1.
CCDSiCCDS10760.1.
RefSeqiNP_008937.1. NM_007006.2.
UniGeneiHs.528834.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2CL3X-ray1.90A21-227[»]
2J8QX-ray2.30A/B24-227[»]
3BAPX-ray1.85A1-227[»]
3BHOX-ray1.80A20-227[»]
3MDGX-ray2.22A/B1-227[»]
3MDIX-ray2.07A/B1-227[»]
3N9UX-ray1.92A/B21-227[»]
3P5TX-ray2.70A/B/C/D/E/F34-227[»]
3P6YX-ray2.90A/B/E/F/I/J/M/N34-227[»]
3Q2SX-ray2.90A/B21-227[»]
3Q2TX-ray3.06A/B21-227[»]
ProteinModelPortaliO43809.
SMRiO43809.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116237. 121 interactors.
DIPiDIP-42502N.
IntActiO43809. 79 interactors.
MINTiMINT-5002263.
STRINGi9606.ENSP00000300291.

PTM databases

iPTMnetiO43809.
PhosphoSitePlusiO43809.
SwissPalmiO43809.

Polymorphism and mutation databases

BioMutaiNUDT21.

2D gel databases

UCD-2DPAGEO43809.

Proteomic databases

EPDiO43809.
MaxQBiO43809.
PaxDbiO43809.
PeptideAtlasiO43809.
PRIDEiO43809.
TopDownProteomicsiO43809.

Protocols and materials databases

DNASUi11051.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000300291; ENSP00000300291; ENSG00000167005.
GeneIDi11051.
KEGGihsa:11051.
UCSCiuc002eja.4. human.

Organism-specific databases

CTDi11051.
DisGeNETi11051.
GeneCardsiNUDT21.
HGNCiHGNC:13870. NUDT21.
HPAiHPA019863.
HPA074228.
MIMi604978. gene.
neXtProtiNX_O43809.
OpenTargetsiENSG00000167005.
PharmGKBiPA26845.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1689. Eukaryota.
ENOG410XS8Z. LUCA.
GeneTreeiENSGT00390000015814.
HOGENOMiHOG000161320.
HOVERGENiHBG052968.
InParanoidiO43809.
KOiK14397.
OMAiGDCLAQW.
OrthoDBiEOG091G0HGL.
PhylomeDBiO43809.
TreeFamiTF106356.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000167005-MONOMER.
ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72187. mRNA 3'-end processing.
R-HSA-77595. Processing of Intronless Pre-mRNAs.

Miscellaneous databases

ChiTaRSiNUDT21. human.
EvolutionaryTraceiO43809.
GeneWikiiNUDT21.
GenomeRNAii11051.
PROiO43809.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000167005.
CleanExiHS_NUDT21.
ExpressionAtlasiO43809. baseline and differential.
GenevisibleiO43809. HS.

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...

Entry informationi

Entry nameiCPSF5_HUMAN
AccessioniPrimary (citable) accession number: O43809
Secondary accession number(s): Q6IB85, Q6NE84
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: June 1, 1998
Last modified: November 30, 2016
This is version 152 of the entry and version 1 of the sequence. [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

Caution

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

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.