A9LNK9 · CPSF_ARATH

Function

function

Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation. May interact with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition (By similarity).
Mediates poly(A) site selection (PubMed:23136375).
Binds RNA in a calcium-dependent manner (PubMed:16500995, PubMed:17576667, PubMed:20214900).
Exhibits endonuclease activity with an ability to nick and degrade linear as well as circular single-stranded RNA that leaves RNA 3' ends with hydroxyl groups, thus mediating processing of the pre-mRNA as a prelude to the polyadenylation (PubMed:17576667).
Involved in the post-transcriptional control, probably via poly(A) addition, of the responses of plants to stress, especially genes mediating tolerance to oxidative stress (PubMed:18545667).
Plays a role in the regulation of salicylic acid (SA) production via the control of messenger RNA 3' end processing, thus being a key component of programmed cell death and plant immune responses required for resistance to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550).

Activity regulation

Endonuclease activity is repressed by the N-terminal domain of FIPS5 (PubMed:17576667).
Nuclease activity is inhibited by zinc (>100 uM), cadmium in a progressive manner (50 percent activity at 1 mM Cd2+), and high salt levels (e.g. KCl or NaCl >600 mM). Stimulated by ATP in the presence of Zn2+, even at inhibitory zinc concentrations. Elevated temperatures prevent RNA-binding at 55 degrees Celsius, but endonuclease activity at 70 degrees Celsius. The sulfhydryl reagent dithiothreitol (DTT) inhibits both RNA-binding and nuclease activities (PubMed:18331819).

GO annotations

AspectTerm
Cellular Componentcytoplasm
Cellular ComponentmRNA cleavage and polyadenylation specificity factor complex
Cellular Componentnucleus
Molecular Functioncalmodulin binding
Molecular FunctionDNA binding
Molecular Functionendonuclease activity
Molecular Functionmetal ion binding
Molecular FunctionmRNA binding
Molecular FunctionRNA binding
Molecular FunctionRNA endonuclease activity
Biological Processapoptotic process
Biological ProcessmRNA 3'-end processing
Biological Processplant-type hypersensitive response
Biological Processpositive regulation of plant-type hypersensitive response
Biological Processpositive regulation of programmed cell death
Biological Processregulation of salicylic acid mediated signaling pathway
Biological Processresponse to oxidative stress
Biological ProcessRNA processing

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    30-kDa cleavage and polyadenylation specificity factor 30
  • EC number
  • Alternative names
    • Protein OXIDATIVE STRESS TOLERANT 6
    • Zinc finger CCCH domain-containing protein 11 (AtC3H11)

Gene names

    • Name
      CPSF30
    • Synonyms
      OXT6
    • ORF names
      F26G16.5
      , F26G16.6
    • Ordered locus names
      At1g30460

Organism names

  • Taxonomic identifier
  • Strain
    • cv. Columbia
  • Taxonomic lineage
    Eukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis

Accessions

  • Primary accession
    A9LNK9
  • Secondary accessions
    • Q9S9Q5
    • Q9S9Q6

Proteomes

Organism-specific databases

Genome annotation databases

Subcellular Location

Nucleus
Cytoplasm
Note: Localized in the cytoplasm when not in complex or when associated with CPSF100, but move to the nucleus when associated with the cleavage and polyadenylation specificity factor (CPSF) subunits CPSF160 or CPSF73s.

Keywords

Phenotypes & Variants

Disruption phenotype

In oxt6, small plants, especially at temperatures above 22 degrees Celsius. Enhanced tolerance to oxidative stress associated with elevated constitutive expression of genes that encode proteins containing thioredoxin- and glutaredoxin- related domains (PubMed:18545667).
Altered poly(A) site choice (PubMed:18545667, PubMed:23136375).
Suppresses cell death in lesion-mimic mutants (e.g. mips1, lsd1, mkk4, cpr5, and cat2). Enhanced sensitivity to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550).

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis80-86Loss of RNA-binding, but normal endonuclease activity.
Mutagenesis108-112Reduced endonuclease activity, but slightly increased RNA-binding.
Mutagenesis134-138Loss of endonuclease activity, slighty reduced RNA-binding, and loss of interaction with FIPS5.

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 30 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

PTM/Processing

Features

Showing features for chain, modified residue.

TypeIDPosition(s)Description
ChainPRO_00003719701-63130-kDa cleavage and polyadenylation specificity factor 30
Modified residue610Phosphoserine
Modified residue612Phosphoserine

Keywords

Proteomic databases

PTM databases

Expression

Tissue specificity

Expressed in seedlings, roots, leaves, siliques, stems and flowers.

Induction

Isoform 2 is up-regulated by exposure to the oxidative agent methyl viologen (MV).

Gene expression databases

Interaction

Subunit

Component of the cleavage and polyadenylation specificity factor (CPSF) complex (Probable). Can form homodimers (PubMed:18479511).
Binds to calmodulin (PubMed:16500995, PubMed:16897494).
Forms a complex with cleavage and polyadenylation specificity factor (CPSF) subunits CPSF73-I, CPSF73-II, CPSF100, CPSF160, CFIS2, FIPS3, FIPS5, PAPS2, PAPS3, CLPS3, PCFS1, PCFS4, CSTF50 and CSTF77 (PubMed:16282318, PubMed:17576667, PubMed:18479511, PubMed:19573236, PubMed:20214900).

Binary interactions

Protein-protein interaction databases

Family & Domains

Features

Showing features for region, compositional bias, zinc finger, domain.

TypeIDPosition(s)Description
Region12-38Disordered
Compositional bias18-38Polar residues
Zinc finger60-87C3H1-type 1
Zinc finger88-112C3H1-type 2
Zinc finger114-141C3H1-type 3
Region179-234Disordered
Domain237-372YTH
Region392-447Disordered
Compositional bias412-432Acidic residues
Region541-631Disordered

Sequence similarities

Belongs to the CPSF4/YTH1 family.

Keywords

Phylogenomic databases

Family and domain databases

Sequence & Isoform

Align isoforms (2)
  • Sequence status
    Complete

This entry describes 2 isoforms produced by Alternative splicing.

A9LNK9-1

This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

  • Name
    1
  • Synonyms
    AtCPSF30-YT521B
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Length
    631
  • Mass (Da)
    70,015
  • Last updated
    2008-02-05 v1
  • Checksum
    120272CD4142355F
MEDADGLSFDFEGGLDSGPVQNTASVPVAPPENSSSAAVNVAPTYDHSSATVAGAGRGRSFRQTVCRHWLRGLCMKGDACGFLHQFDKARMPICRFFRLYGECREQDCVYKHTNEDIKECNMYKLGFCPNGPDCRYRHAKLPGPPPPVEEVLQKIQQLTTYNYGTNRLYQARNVAPQLQDRPQGQVPMQGQPQESGNLQQQQQQQPQQSQHQVSQTLIPNPADQTNRTSHPLPQGVNRYFVVKSNNRENFELSVQQGVWATQRSNEAKLNEAFDSVENVILIFSVNRTRHFQGCAKMTSRIGGYIGGGNWKHEHGTAQYGRNFSVKWLKLCELSFHKTRNLRNPYNENLPVKISRDCQELEPSVGEQLASLLYLEPDSELMAISIAAEAKREEEKAKGVNPESRAENPDIVPFEDNEEEEEEEDESEEEEESMAGGPQGRGRGRGIMWPPQMPLGRGIRPMPGMGGFPLGVMGPGDAFPYGPGGYNGMPDPFGMGPRPFGPYGPRFGGDFRGPVPGMMFPGRPPQQFPHGGYGMMGGGRGPHMGGMGNAPRGGRPMYYPPATSSARPGPSNRKTPERSDERGVSGDQQNQDASHDMEQFEVGNSLRNEESESEDEDEAPRRSRHGEGKKRR

A9LNK9-2

  • Name
    2
  • Synonyms
    AtCPSF30
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Computationally mapped potential isoform sequences

There are 2 potential isoforms mapped to this entry

View all
EntryEntry nameGene nameLength
A0A1P8AQZ1A0A1P8AQZ1_ARATHCPSF30244
A0A2H1ZEB9A0A2H1ZEB9_ARATHCPSF30401

Sequence caution

The sequence AAF19746.1 differs from that shown. Reason: Erroneous gene model prediction

Features

Showing features for compositional bias, alternative sequence.

TypeIDPosition(s)Description
Compositional bias18-38Polar residues
Alternative sequenceVSP_037127239-250in isoform 2
Alternative sequenceVSP_037128251-631in isoform 2
Compositional bias412-432Acidic residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
EU250988
EMBL· GenBank· DDBJ
ABX26048.1
EMBL· GenBank· DDBJ
mRNA
AY140901
EMBL· GenBank· DDBJ
AAN41459.1
EMBL· GenBank· DDBJ
mRNA
AC009917
EMBL· GenBank· DDBJ
AAF19746.1
EMBL· GenBank· DDBJ
Genomic DNA Sequence problems.
AC009917
EMBL· GenBank· DDBJ
AAF19747.1
EMBL· GenBank· DDBJ
Genomic DNA
CP002684
EMBL· GenBank· DDBJ
AEE31221.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

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