UniProtKB - Q9GZU7 (CTDS1_HUMAN)
Protein
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
Gene
CTDSP1
Organism
Homo sapiens (Human)
Status
Functioni
Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells.2 Publications
Catalytic activityi
Cofactori
Mg2+1 PublicationNote: Binds 1 Mg2+ ion per monomer.2 Publications
Activity regulationi
Stimulated by GTF2F1. Inhibited by beryllofluoride anions.1 Publication
pH dependencei
Optimum pH is 5.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Active sitei | 96 | 4-aspartylphosphate intermediate2 Publications | 1 | |
Metal bindingi | 96 | Magnesium1 Publication | 1 | |
Active sitei | 98 | Proton donor1 Publication | 1 | |
Metal bindingi | 98 | Magnesium; via carbonyl oxygen1 Publication | 1 | |
Sitei | 152 | Transition state stabilizer1 Publication | 1 | |
Sitei | 190 | Transition state stabilizer1 Publication | 1 | |
Metal bindingi | 207 | Magnesium1 Publication | 1 |
GO - Molecular functioni
- metal ion binding Source: UniProtKB-KW
- phosphoprotein phosphatase activity Source: GO_Central
- protein serine phosphatase activity Source: UniProtKB-EC
- protein threonine phosphatase activity Source: UniProtKB-EC
- RNA polymerase II CTD heptapeptide repeat phosphatase activity Source: UniProtKB
GO - Biological processi
- protein dephosphorylation Source: UniProtKB
- regulation of transcription by RNA polymerase II Source: UniProtKB
Keywordsi
Molecular function | Hydrolase, Protein phosphatase |
Ligand | Magnesium, Metal-binding |
Enzyme and pathway databases
PathwayCommonsi | Q9GZU7 |
SignaLinki | Q9GZU7 |
SIGNORi | Q9GZU7 |
Names & Taxonomyi
Protein namesi | Recommended name: Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC:3.1.3.162 Publications)Alternative name(s): Nuclear LIM interactor-interacting factor 3 Short name: NLI-IF Short name: NLI-interacting factor 3 Small C-terminal domain phosphatase 1 Short name: SCP1 Short name: Small CTD phosphatase 1 |
Gene namesi | Name:CTDSP1 Synonyms:NIF3, NLIIF, SCP1 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:21614, CTDSP1 |
MIMi | 605323, gene |
neXtProti | NX_Q9GZU7 |
VEuPathDBi | HostDB:ENSG00000144579.7 |
Subcellular locationi
Nucleus
- Nucleus 1 Publication
Note: Colocalizes with RNA polymerase II.
Extracellular region or secreted
- extracellular exosome Source: UniProtKB
Nucleus
- nucleoplasm Source: HPA
- nucleus Source: UniProtKB
Keywords - Cellular componenti
NucleusPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 96 | D → E: No effect. Completely abolishes phosphatase activity; when associated with N-98. 1 Publication | 1 | |
Mutagenesisi | 98 | D → N: Completely abolishes phosphatase activity; when associated with E-96. 1 Publication | 1 |
Organism-specific databases
DisGeNETi | 58190 |
OpenTargetsi | ENSG00000144579 |
PharmGKBi | PA134938848 |
Miscellaneous databases
Pharosi | Q9GZU7, Tbio |
Chemistry databases
ChEMBLi | CHEMBL1795098 |
DrugBanki | DB04156, Aspartate Beryllium Trifluoride DB04272, Citric acid |
Genetic variation databases
BioMutai | CTDSP1 |
DMDMi | 17865510 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000212572 | 1 – 261 | Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1Add BLAST | 261 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1 | N-acetylmethionineCombined sources | 1 |
Keywords - PTMi
AcetylationProteomic databases
EPDi | Q9GZU7 |
jPOSTi | Q9GZU7 |
MassIVEi | Q9GZU7 |
MaxQBi | Q9GZU7 |
PaxDbi | Q9GZU7 |
PeptideAtlasi | Q9GZU7 |
PRIDEi | Q9GZU7 |
ProteomicsDBi | 7655 80150 [Q9GZU7-1] 80151 [Q9GZU7-2] |
PTM databases
DEPODi | CTDSP1 |
iPTMneti | Q9GZU7 |
PhosphoSitePlusi | Q9GZU7 |
SwissPalmi | Q9GZU7 |
Expressioni
Tissue specificityi
Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta.1 Publication
Gene expression databases
Bgeei | ENSG00000144579, Expressed in stomach and 230 other tissues |
ExpressionAtlasi | Q9GZU7, baseline and differential |
Genevisiblei | Q9GZU7, HS |
Organism-specific databases
HPAi | ENSG00000144579, Low tissue specificity |
Interactioni
Subunit structurei
Monomer (By similarity).
Interacts with GTF2F1.
Interacts with REST.
By similarity4 PublicationsBinary interactionsi
Hide detailsQ9GZU7
Protein-protein interaction databases
BioGRIDi | 121804, 59 interactors |
DIPi | DIP-61246N |
IntActi | Q9GZU7, 41 interactors |
MINTi | Q9GZU7 |
STRINGi | 9606.ENSP00000273062 |
Chemistry databases
BindingDBi | Q9GZU7 |
Miscellaneous databases
RNActi | Q9GZU7, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q9GZU7 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9GZU7 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 86 – 244 | FCP1 homologyPROSITE-ProRule annotationAdd BLAST | 159 |
Phylogenomic databases
eggNOGi | KOG1605, Eukaryota |
GeneTreei | ENSGT00990000203506 |
InParanoidi | Q9GZU7 |
OrthoDBi | 1176152at2759 |
PhylomeDBi | Q9GZU7 |
TreeFami | TF313556 |
Family and domain databases
Gene3Di | 3.40.50.1000, 1 hit |
IDEALi | IID00394 |
InterProi | View protein in InterPro IPR011948, Dullard_phosphatase IPR004274, FCP1_dom IPR036412, HAD-like_sf IPR023214, HAD_sf IPR040078, RNA_Pol_CTD_Phosphatase |
Pfami | View protein in Pfam PF03031, NIF, 1 hit |
SFLDi | SFLDG01124, C0.1:_RNA_Pol_CTD_Phosphatase, 1 hit |
SMARTi | View protein in SMART SM00577, CPDc, 1 hit |
SUPFAMi | SSF56784, SSF56784, 1 hit |
TIGRFAMsi | TIGR02251, HIF-SF_euk, 1 hit |
PROSITEi | View protein in PROSITE PS50969, FCP1, 1 hit |
s (3+)i Sequence
Sequence statusi: Complete.
This entry describes 3 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 3 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All
Isoform 1 (identifier: Q9GZU7-1) [UniParc]FASTAAdd to basket
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MDSSAVITQI SKEEARGPLR GKGDQKSAAS QKPRSRGILH SLFCCVCRDD
60 70 80 90 100
GEALPAHSGA PLLVEENGAI PKQTPVQYLL PEAKAQDSDK ICVVIDLDET
110 120 130 140 150
LVHSSFKPVN NADFIIPVEI DGVVHQVYVL KRPHVDEFLQ RMGELFECVL
160 170 180 190 200
FTASLAKYAD PVADLLDKWG AFRARLFRES CVFHRGNYVK DLSRLGRDLR
210 220 230 240 250
RVLILDNSPA SYVFHPDNAV PVASWFDNMS DTELHDLLPF FEQLSRVDDV
260
YSVLRQPRPG S
Computationally mapped potential isoform sequencesi
There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketH7C1Z7 | H7C1Z7_HUMAN | Protein-serine/threonine phosphatas... | CTDSP1 | 262 | Annotation score: | ||
H7C270 | H7C270_HUMAN | Protein-serine/threonine phosphatas... | CTDSP1 | 254 | Annotation score: | ||
H7C3E0 | H7C3E0_HUMAN | Carboxy-terminal domain RNA polymer... | CTDSP1 | 195 | Annotation score: |
Sequence cautioni
The sequence AAP34398 differs from that shown. Reason: Frameshift.Curated
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 180 | S → F in BX446444 (Ref. 3) Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_049054 | 56 | A → T. Corresponds to variant dbSNP:rs2227249EnsemblClinVar. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_045865 | 1 – 22 | MDSSA…PLRGK → MVAAPWATQEQEEGRGIQPG DR in isoform 3. 1 PublicationAdd BLAST | 22 | |
Alternative sequenceiVSP_045866 | 73 | Missing in isoform 2 and isoform 3. 2 Publications | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF229163 Genomic DNA Translation: AAG15404.1 AF229162 mRNA Translation: AAG15402.1 AY279529 mRNA Translation: AAP34397.1 AY279530 mRNA Translation: AAP34398.1 Frameshift. BX446444 mRNA No translation available. AC021016 Genomic DNA No translation available. BC012977 mRNA Translation: AAH12977.1 |
CCDSi | CCDS2416.1 [Q9GZU7-1] CCDS56166.1 [Q9GZU7-3] |
RefSeqi | NP_001193807.1, NM_001206878.1 [Q9GZU7-3] NP_067021.1, NM_021198.2 [Q9GZU7-1] NP_872580.1, NM_182642.2 [Q9GZU7-2] |
Genome annotation databases
Ensembli | ENST00000273062; ENSP00000273062; ENSG00000144579 [Q9GZU7-1] ENST00000443891; ENSP00000392248; ENSG00000144579 [Q9GZU7-3] |
GeneIDi | 58190 |
KEGGi | hsa:58190 |
UCSCi | uc002vhy.3, human [Q9GZU7-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF229163 Genomic DNA Translation: AAG15404.1 AF229162 mRNA Translation: AAG15402.1 AY279529 mRNA Translation: AAP34397.1 AY279530 mRNA Translation: AAP34398.1 Frameshift. BX446444 mRNA No translation available. AC021016 Genomic DNA No translation available. BC012977 mRNA Translation: AAH12977.1 |
CCDSi | CCDS2416.1 [Q9GZU7-1] CCDS56166.1 [Q9GZU7-3] |
RefSeqi | NP_001193807.1, NM_001206878.1 [Q9GZU7-3] NP_067021.1, NM_021198.2 [Q9GZU7-1] NP_872580.1, NM_182642.2 [Q9GZU7-2] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1T9Z | X-ray | 2.30 | A | 77-261 | [»] | |
1TA0 | X-ray | 2.10 | A | 77-261 | [»] | |
2GHQ | X-ray | 2.05 | A/B | 77-256 | [»] | |
2GHT | X-ray | 1.80 | A/B | 77-256 | [»] | |
3L0B | X-ray | 2.35 | A/B | 77-256 | [»] | |
3L0C | X-ray | 2.45 | A/B | 77-256 | [»] | |
3L0Y | X-ray | 2.30 | A/B | 77-256 | [»] | |
3PGL | X-ray | 2.35 | A/B | 77-256 | [»] | |
4YGY | X-ray | 2.36 | A/B | 77-261 | [»] | |
4YH1 | X-ray | 2.20 | A/B | 77-255 | [»] | |
6DU3 | X-ray | 2.58 | A/B | 77-256 | [»] | |
SMRi | Q9GZU7 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 121804, 59 interactors |
DIPi | DIP-61246N |
IntActi | Q9GZU7, 41 interactors |
MINTi | Q9GZU7 |
STRINGi | 9606.ENSP00000273062 |
Chemistry databases
BindingDBi | Q9GZU7 |
ChEMBLi | CHEMBL1795098 |
DrugBanki | DB04156, Aspartate Beryllium Trifluoride DB04272, Citric acid |
PTM databases
DEPODi | CTDSP1 |
iPTMneti | Q9GZU7 |
PhosphoSitePlusi | Q9GZU7 |
SwissPalmi | Q9GZU7 |
Genetic variation databases
BioMutai | CTDSP1 |
DMDMi | 17865510 |
Proteomic databases
EPDi | Q9GZU7 |
jPOSTi | Q9GZU7 |
MassIVEi | Q9GZU7 |
MaxQBi | Q9GZU7 |
PaxDbi | Q9GZU7 |
PeptideAtlasi | Q9GZU7 |
PRIDEi | Q9GZU7 |
ProteomicsDBi | 7655 80150 [Q9GZU7-1] 80151 [Q9GZU7-2] |
Protocols and materials databases
Antibodypediai | 34272, 395 antibodies |
DNASUi | 58190 |
Genome annotation databases
Ensembli | ENST00000273062; ENSP00000273062; ENSG00000144579 [Q9GZU7-1] ENST00000443891; ENSP00000392248; ENSG00000144579 [Q9GZU7-3] |
GeneIDi | 58190 |
KEGGi | hsa:58190 |
UCSCi | uc002vhy.3, human [Q9GZU7-1] |
Organism-specific databases
CTDi | 58190 |
DisGeNETi | 58190 |
GeneCardsi | CTDSP1 |
HGNCi | HGNC:21614, CTDSP1 |
HPAi | ENSG00000144579, Low tissue specificity |
MIMi | 605323, gene |
neXtProti | NX_Q9GZU7 |
OpenTargetsi | ENSG00000144579 |
PharmGKBi | PA134938848 |
VEuPathDBi | HostDB:ENSG00000144579.7 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1605, Eukaryota |
GeneTreei | ENSGT00990000203506 |
InParanoidi | Q9GZU7 |
OrthoDBi | 1176152at2759 |
PhylomeDBi | Q9GZU7 |
TreeFami | TF313556 |
Enzyme and pathway databases
PathwayCommonsi | Q9GZU7 |
SignaLinki | Q9GZU7 |
SIGNORi | Q9GZU7 |
Miscellaneous databases
BioGRID-ORCSi | 58190, 24 hits in 877 CRISPR screens |
ChiTaRSi | CTDSP1, human |
EvolutionaryTracei | Q9GZU7 |
GeneWikii | CTDSP1 |
GenomeRNAii | 58190 |
Pharosi | Q9GZU7, Tbio |
PROi | PR:Q9GZU7 |
RNActi | Q9GZU7, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000144579, Expressed in stomach and 230 other tissues |
ExpressionAtlasi | Q9GZU7, baseline and differential |
Genevisiblei | Q9GZU7, HS |
Family and domain databases
Gene3Di | 3.40.50.1000, 1 hit |
IDEALi | IID00394 |
InterProi | View protein in InterPro IPR011948, Dullard_phosphatase IPR004274, FCP1_dom IPR036412, HAD-like_sf IPR023214, HAD_sf IPR040078, RNA_Pol_CTD_Phosphatase |
Pfami | View protein in Pfam PF03031, NIF, 1 hit |
SFLDi | SFLDG01124, C0.1:_RNA_Pol_CTD_Phosphatase, 1 hit |
SMARTi | View protein in SMART SM00577, CPDc, 1 hit |
SUPFAMi | SSF56784, SSF56784, 1 hit |
TIGRFAMsi | TIGR02251, HIF-SF_euk, 1 hit |
PROSITEi | View protein in PROSITE PS50969, FCP1, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | CTDS1_HUMAN | |
Accessioni | Q9GZU7Primary (citable) accession number: Q9GZU7 Secondary accession number(s): C9IYG0, Q7Z5Q3, Q7Z5Q4 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 13, 2001 |
Last sequence update: | March 1, 2001 | |
Last modified: | February 10, 2021 | |
This is version 171 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Human chromosome 2
Human chromosome 2: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references