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Protein

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1

Gene

CTDSP1

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

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

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

Cofactori

Mg2+Note: Binds 1 Mg2+ ion per monomer.

Enzyme regulationi

Stimulated by GTF2F1. Inhibited by beryllofluoride anions.1 Publication

pH dependencei

Optimum pH is 5.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei964-aspartylphosphate intermediate1
Metal bindingi96Magnesium1 Publication1
Active sitei98Proton donor1
Metal bindingi98Magnesium; via carbonyl oxygen1 Publication1
Sitei152Transition state stabilizer1
Sitei190Transition state stabilizer1
Metal bindingi207Magnesium1 Publication1

GO - Molecular functioni

  • CTD phosphatase activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS07180-MONOMER.
SignaLinkiQ9GZU7.
SIGNORiQ9GZU7.

Names & Taxonomyi

Protein namesi
Recommended name:
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC:3.1.3.16)
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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:21614. CTDSP1.

Subcellular locationi

  • Nucleus 1 Publication

  • Note: Colocalizes with RNA polymerase II.

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi96D → E: No effect. Completely abolishes phosphatase activity; when associated with N-98. 1 Publication1
Mutagenesisi98D → N: Completely abolishes phosphatase activity; when associated with E-96. 1 Publication1

Organism-specific databases

DisGeNETi58190.
OpenTargetsiENSG00000144579.
PharmGKBiPA134938848.

Chemistry databases

ChEMBLiCHEMBL1795098.

Polymorphism and mutation databases

BioMutaiCTDSP1.
DMDMi17865510.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002125721 – 261Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1Add BLAST261

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ9GZU7.
MaxQBiQ9GZU7.
PaxDbiQ9GZU7.
PeptideAtlasiQ9GZU7.
PRIDEiQ9GZU7.

PTM databases

DEPODiQ9GZU7.
iPTMnetiQ9GZU7.
PhosphoSitePlusiQ9GZU7.
SwissPalmiQ9GZU7.

Expressioni

Tissue specificityi

Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta.1 Publication

Gene expression databases

BgeeiENSG00000144579.
CleanExiHS_CTDSP1.
ExpressionAtlasiQ9GZU7. baseline and differential.
GenevisibleiQ9GZU7. HS.

Organism-specific databases

HPAiHPA062654.

Interactioni

Subunit structurei

Monomer (By similarity). Interacts with GTF2F1. Interacts with REST.By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDCA3Q996186EBI-751587,EBI-739534
Ctdsp1P584662EBI-751587,EBI-7091612From a different organism.
MBPP026863EBI-751587,EBI-947410

Protein-protein interaction databases

BioGridi121804. 16 interactors.
DIPiDIP-61246N.
IntActiQ9GZU7. 4 interactors.
MINTiMINT-1441843.
STRINGi9606.ENSP00000273062.

Chemistry databases

BindingDBiQ9GZU7.

Structurei

Secondary structure

1261
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi85 – 87Combined sources3
Beta strandi92 – 95Combined sources4
Turni99 – 101Combined sources3
Beta strandi102 – 107Combined sources6
Beta strandi113 – 120Combined sources8
Beta strandi123 – 131Combined sources9
Helixi135 – 145Combined sources11
Beta strandi146 – 151Combined sources6
Helixi156 – 166Combined sources11
Beta strandi172 – 176Combined sources5
Helixi178 – 180Combined sources3
Beta strandi181 – 184Combined sources4
Beta strandi187 – 189Combined sources3
Helixi192 – 194Combined sources3
Beta strandi195 – 197Combined sources3
Helixi199 – 201Combined sources3
Beta strandi202 – 205Combined sources4
Helixi209 – 212Combined sources4
Helixi216 – 218Combined sources3
Beta strandi219 – 221Combined sources3
Helixi233 – 244Combined sources12
Helixi251 – 254Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T9ZX-ray2.30A77-261[»]
1TA0X-ray2.10A77-261[»]
2GHQX-ray2.05A/B77-256[»]
2GHTX-ray1.80A/B77-256[»]
3L0BX-ray2.35A/B77-256[»]
3L0CX-ray2.45A/B77-256[»]
3L0YX-ray2.30A/B77-256[»]
3PGLX-ray2.35A/B77-256[»]
4YGYX-ray2.36A/B77-261[»]
4YH1X-ray2.20A/B77-255[»]
ProteinModelPortaliQ9GZU7.
SMRiQ9GZU7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9GZU7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini86 – 244FCP1 homologyPROSITE-ProRule annotationAdd BLAST159

Sequence similaritiesi

Contains 1 FCP1 homology domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1605. Eukaryota.
COG5190. LUCA.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiQ9GZU7.
KOiK15731.
PhylomeDBiQ9GZU7.
TreeFamiTF313556.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR011948. Dullard_phosphatase.
IPR004274. FCP1_dom.
IPR023214. HAD-like_dom.
[Graphical view]
PfamiPF03031. NIF. 1 hit.
[Graphical view]
SMARTiSM00577. CPDc. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR02251. HIF-SF_euk. 1 hit.
PROSITEiPS50969. FCP1. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9GZU7-1) [UniParc]FASTAAdd to basket

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.

« Hide

        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
Length:261
Mass (Da):29,203
Last modified:March 1, 2001 - v1
Checksum:i75A430BCA2748FEA
GO
Isoform 2 (identifier: Q9GZU7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     73-73: Missing.

Show »
Length:260
Mass (Da):29,075
Checksum:i30B0CCD745F26DBB
GO
Isoform 3 (identifier: Q9GZU7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-22: MDSSAVITQISKEEARGPLRGK → MVAAPWATQEQEEGRGIQPGDR
     73-73: Missing.

Note: No experimental confirmation available.
Show »
Length:260
Mass (Da):29,128
Checksum:iD7741284DEE4D3B5
GO

Sequence cautioni

The sequence AAP34398 differs from that shown. Reason: Frameshift at position 72.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti180S → F in BX446444 (Ref. 3) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04905456A → T.Corresponds to variant rs2227249dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0458651 – 22MDSSA…PLRGK → MVAAPWATQEQEEGRGIQPG DR in isoform 3. 1 PublicationAdd BLAST22
Alternative sequenceiVSP_04586673Missing in isoform 2 and isoform 3. 2 Publications1

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.
CCDSiCCDS2416.1. [Q9GZU7-1]
CCDS56166.1. [Q9GZU7-3]
RefSeqiNP_001193807.1. NM_001206878.1. [Q9GZU7-3]
NP_067021.1. NM_021198.2. [Q9GZU7-1]
NP_872580.1. NM_182642.2. [Q9GZU7-2]
UniGeneiHs.444468.

Genome annotation databases

EnsembliENST00000273062; ENSP00000273062; ENSG00000144579. [Q9GZU7-1]
ENST00000443891; ENSP00000392248; ENSG00000144579. [Q9GZU7-3]
GeneIDi58190.
KEGGihsa:58190.
UCSCiuc002vhy.3. human. [Q9GZU7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

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.
CCDSiCCDS2416.1. [Q9GZU7-1]
CCDS56166.1. [Q9GZU7-3]
RefSeqiNP_001193807.1. NM_001206878.1. [Q9GZU7-3]
NP_067021.1. NM_021198.2. [Q9GZU7-1]
NP_872580.1. NM_182642.2. [Q9GZU7-2]
UniGeneiHs.444468.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1T9ZX-ray2.30A77-261[»]
1TA0X-ray2.10A77-261[»]
2GHQX-ray2.05A/B77-256[»]
2GHTX-ray1.80A/B77-256[»]
3L0BX-ray2.35A/B77-256[»]
3L0CX-ray2.45A/B77-256[»]
3L0YX-ray2.30A/B77-256[»]
3PGLX-ray2.35A/B77-256[»]
4YGYX-ray2.36A/B77-261[»]
4YH1X-ray2.20A/B77-255[»]
ProteinModelPortaliQ9GZU7.
SMRiQ9GZU7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121804. 16 interactors.
DIPiDIP-61246N.
IntActiQ9GZU7. 4 interactors.
MINTiMINT-1441843.
STRINGi9606.ENSP00000273062.

Chemistry databases

BindingDBiQ9GZU7.
ChEMBLiCHEMBL1795098.

PTM databases

DEPODiQ9GZU7.
iPTMnetiQ9GZU7.
PhosphoSitePlusiQ9GZU7.
SwissPalmiQ9GZU7.

Polymorphism and mutation databases

BioMutaiCTDSP1.
DMDMi17865510.

Proteomic databases

EPDiQ9GZU7.
MaxQBiQ9GZU7.
PaxDbiQ9GZU7.
PeptideAtlasiQ9GZU7.
PRIDEiQ9GZU7.

Protocols and materials databases

DNASUi58190.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000273062; ENSP00000273062; ENSG00000144579. [Q9GZU7-1]
ENST00000443891; ENSP00000392248; ENSG00000144579. [Q9GZU7-3]
GeneIDi58190.
KEGGihsa:58190.
UCSCiuc002vhy.3. human. [Q9GZU7-1]

Organism-specific databases

CTDi58190.
DisGeNETi58190.
GeneCardsiCTDSP1.
HGNCiHGNC:21614. CTDSP1.
HPAiHPA062654.
MIMi605323. gene.
neXtProtiNX_Q9GZU7.
OpenTargetsiENSG00000144579.
PharmGKBiPA134938848.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1605. Eukaryota.
COG5190. LUCA.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiQ9GZU7.
KOiK15731.
PhylomeDBiQ9GZU7.
TreeFamiTF313556.

Enzyme and pathway databases

BioCyciZFISH:HS07180-MONOMER.
SignaLinkiQ9GZU7.
SIGNORiQ9GZU7.

Miscellaneous databases

ChiTaRSiCTDSP1. human.
EvolutionaryTraceiQ9GZU7.
GeneWikiiCTDSP1.
GenomeRNAii58190.
PROiQ9GZU7.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000144579.
CleanExiHS_CTDSP1.
ExpressionAtlasiQ9GZU7. baseline and differential.
GenevisibleiQ9GZU7. HS.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR011948. Dullard_phosphatase.
IPR004274. FCP1_dom.
IPR023214. HAD-like_dom.
[Graphical view]
PfamiPF03031. NIF. 1 hit.
[Graphical view]
SMARTiSM00577. CPDc. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR02251. HIF-SF_euk. 1 hit.
PROSITEiPS50969. FCP1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCTDS1_HUMAN
AccessioniPrimary (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: November 30, 2016
This is version 141 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.