A9LNK9 · CPSF_ARATH
- Protein30-kDa cleavage and polyadenylation specificity factor 30
- GeneCPSF30
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids631 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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).
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
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Cellular Component | mRNA cleavage and polyadenylation specificity factor complex | |
Cellular Component | nucleus | |
Molecular Function | calmodulin binding | |
Molecular Function | DNA binding | |
Molecular Function | endonuclease activity | |
Molecular Function | metal ion binding | |
Molecular Function | mRNA binding | |
Molecular Function | RNA binding | |
Molecular Function | RNA endonuclease activity | |
Biological Process | apoptotic process | |
Biological Process | mRNA 3'-end processing | |
Biological Process | plant-type hypersensitive response | |
Biological Process | positive regulation of plant-type hypersensitive response | |
Biological Process | positive regulation of programmed cell death | |
Biological Process | regulation of salicylic acid mediated signaling pathway | |
Biological Process | response to oxidative stress | |
Biological Process | RNA processing |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended name30-kDa cleavage and polyadenylation specificity factor 30
- EC number
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageEukaryota > Viridiplantae > Streptophyta > Embryophyta > Tracheophyta > Spermatophyta > Magnoliopsida > eudicotyledons > Gunneridae > Pentapetalae > rosids > malvids > Brassicales > Brassicaceae > Camelineae > Arabidopsis
Accessions
- Primary accessionA9LNK9
- Secondary accessions
Proteomes
Organism-specific databases
Genome annotation databases
Subcellular Location
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).
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 80-86 | Loss of RNA-binding, but normal endonuclease activity. | ||||
Sequence: CGFLHQF → STFLYQ | ||||||
Mutagenesis | 108-112 | Reduced endonuclease activity, but slightly increased RNA-binding. | ||||
Sequence: CVYKH → QDSTYKY | ||||||
Mutagenesis | 134-138 | Loss of endonuclease activity, slighty reduced RNA-binding, and loss of interaction with FIPS5. | ||||
Sequence: CRYRH → STYRY |
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.
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000371970 | 1-631 | 30-kDa cleavage and polyadenylation specificity factor 30 | |||
Sequence: MEDADGLSFDFEGGLDSGPVQNTASVPVAPPENSSSAAVNVAPTYDHSSATVAGAGRGRSFRQTVCRHWLRGLCMKGDACGFLHQFDKARMPICRFFRLYGECREQDCVYKHTNEDIKECNMYKLGFCPNGPDCRYRHAKLPGPPPPVEEVLQKIQQLTTYNYGTNRLYQARNVAPQLQDRPQGQVPMQGQPQESGNLQQQQQQQPQQSQHQVSQTLIPNPADQTNRTSHPLPQGVNRYFVVKSNNRENFELSVQQGVWATQRSNEAKLNEAFDSVENVILIFSVNRTRHFQGCAKMTSRIGGYIGGGNWKHEHGTAQYGRNFSVKWLKLCELSFHKTRNLRNPYNENLPVKISRDCQELEPSVGEQLASLLYLEPDSELMAISIAAEAKREEEKAKGVNPESRAENPDIVPFEDNEEEEEEEDESEEEEESMAGGPQGRGRGRGIMWPPQMPLGRGIRPMPGMGGFPLGVMGPGDAFPYGPGGYNGMPDPFGMGPRPFGPYGPRFGGDFRGPVPGMMFPGRPPQQFPHGGYGMMGGGRGPHMGGMGNAPRGGRPMYYPPATSSARPGPSNRKTPERSDERGVSGDQQNQDASHDMEQFEVGNSLRNEESESEDEDEAPRRSRHGEGKKRR | ||||||
Modified residue | 610 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 612 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
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).
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
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | A9LNK9 | CPSF100 Q9LKF9 | 3 | EBI-962511, EBI-1775444 | |
BINARY | A9LNK9 | CSTF77 Q8GUP1 | 2 | EBI-962511, EBI-1775543 | |
BINARY | A9LNK9 | FIPS5 F4KDH9 | 3 | EBI-962511, EBI-962489 | |
BINARY | A9LNK9 | MAK3 O80438 | 3 | EBI-962511, EBI-15205450 | |
BINARY | A9LNK9 | NFYA4 Q8VY64 | 4 | EBI-962511, EBI-4461713 | |
BINARY | A9LNK9 | PAPS2 O82312 | 3 | EBI-962511, EBI-1775513 | |
BINARY | A9LNK9 | RFI2 O82239 | 3 | EBI-962511, EBI-4425094 | |
BINARY | A9LNK9 | TCP13 Q9S7W5 | 3 | EBI-962511, EBI-4424877 | |
BINARY | A9LNK9 | TCP14 Q93Z00 | 3 | EBI-962511, EBI-4424563 | |
BINARY | A9LNK9 | TCP15 Q9C9L2 | 3 | EBI-962511, EBI-4426144 | |
BINARY | A9LNK9 | TCP23 Q9LQF0 | 3 | EBI-962511, EBI-15192297 | |
BINARY | A9LNK9 | TCP4 Q8LPR5 | 4 | EBI-962511, EBI-15192325 |
Protein-protein interaction databases
Structure
Family & Domains
Features
Showing features for region, compositional bias, zinc finger, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 12-38 | Disordered | ||||
Sequence: EGGLDSGPVQNTASVPVAPPENSSSAA | ||||||
Compositional bias | 18-38 | Polar residues | ||||
Sequence: GPVQNTASVPVAPPENSSSAA | ||||||
Zinc finger | 60-87 | C3H1-type 1 | ||||
Sequence: SFRQTVCRHWLRGLCMKGDACGFLHQFD | ||||||
Zinc finger | 88-112 | C3H1-type 2 | ||||
Sequence: KARMPICRFFRLYGECREQDCVYKH | ||||||
Zinc finger | 114-141 | C3H1-type 3 | ||||
Sequence: NEDIKECNMYKLGFCPNGPDCRYRHAKL | ||||||
Region | 179-234 | Disordered | ||||
Sequence: QDRPQGQVPMQGQPQESGNLQQQQQQQPQQSQHQVSQTLIPNPADQTNRTSHPLPQ | ||||||
Domain | 237-372 | YTH | ||||
Sequence: NRYFVVKSNNRENFELSVQQGVWATQRSNEAKLNEAFDSVENVILIFSVNRTRHFQGCAKMTSRIGGYIGGGNWKHEHGTAQYGRNFSVKWLKLCELSFHKTRNLRNPYNENLPVKISRDCQELEPSVGEQLASLL | ||||||
Region | 392-447 | Disordered | ||||
Sequence: EEEKAKGVNPESRAENPDIVPFEDNEEEEEEEDESEEEEESMAGGPQGRGRGRGIM | ||||||
Compositional bias | 412-432 | Acidic residues | ||||
Sequence: PFEDNEEEEEEEDESEEEEES | ||||||
Region | 541-631 | Disordered | ||||
Sequence: PHMGGMGNAPRGGRPMYYPPATSSARPGPSNRKTPERSDERGVSGDQQNQDASHDMEQFEVGNSLRNEESESEDEDEAPRRSRHGEGKKRR |
Sequence similarities
Belongs to the CPSF4/YTH1 family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence & Isoform
- Sequence statusComplete
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.
- Name1
- SynonymsAtCPSF30-YT521B
- Length631
- Mass (Da)70,015
- Last updated2008-02-05 v1
- Checksum120272CD4142355F
A9LNK9-2
- Name2
- SynonymsAtCPSF30
Computationally mapped potential isoform sequences
There are 2 potential isoforms mapped to this entry
Entry | Entry name | Gene name | Length | ||
---|---|---|---|---|---|
A0A1P8AQZ1 | A0A1P8AQZ1_ARATH | CPSF30 | 244 | ||
A0A2H1ZEB9 | A0A2H1ZEB9_ARATH | CPSF30 | 401 |
Sequence caution
Features
Showing features for compositional bias, alternative sequence.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 18-38 | Polar residues | ||||
Sequence: GPVQNTASVPVAPPENSSSAA | ||||||
Alternative sequence | VSP_037127 | 239-250 | in isoform 2 | |||
Sequence: YFVVKSNNRENF → CVQSPKVFNWVL | ||||||
Alternative sequence | VSP_037128 | 251-631 | in isoform 2 | |||
Sequence: Missing | ||||||
Compositional bias | 412-432 | Acidic residues | ||||
Sequence: PFEDNEEEEEEEDESEEEEES |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |