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Q9GZU7

- CTDS1_HUMAN

UniProt

Q9GZU7 - CTDS1_HUMAN

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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: 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 Mg(2+) 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei96 – 9614-aspartylphosphate intermediate
Metal bindingi96 – 961Magnesium1 Publication
Active sitei98 – 981Proton donor
Metal bindingi98 – 981Magnesium; via carbonyl oxygen1 Publication
Sitei152 – 1521Transition state stabilizer
Sitei190 – 1901Transition state stabilizer
Metal bindingi207 – 2071Magnesium1 Publication

GO - Molecular functioni

  1. CTD phosphatase activity Source: UniProtKB
  2. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. negative regulation of neurogenesis Source: Ensembl
  2. negative regulation of neuron differentiation Source: Ensembl
  3. protein dephosphorylation Source: UniProtKB
  4. regulation of transcription from RNA polymerase II promoter Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

SignaLinkiQ9GZU7.

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
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:21614. CTDSP1.

Subcellular locationi

Nucleus 1 Publication
Note: Colocalizes with RNA polymerase II.

GO - Cellular componenti

  1. extracellular vesicular exosome Source: UniProtKB
  2. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi96 – 961D → E: No effect. Completely abolishes phosphatase activity; when associated with N-98. 1 Publication
Mutagenesisi98 – 981D → N: Completely abolishes phosphatase activity; when associated with E-96. 1 Publication

Organism-specific databases

PharmGKBiPA134938848.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 261261Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1PRO_0000212572Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9GZU7.
PaxDbiQ9GZU7.
PRIDEiQ9GZU7.

PTM databases

PhosphoSiteiQ9GZU7.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiQ9GZU7.
CleanExiHS_CTDSP1.
GenevestigatoriQ9GZU7.

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
Ctdsp1P584662EBI-751587,EBI-7091612From a different organism.

Protein-protein interaction databases

BioGridi121804. 14 interactions.
IntActiQ9GZU7. 2 interactions.
MINTiMINT-1441843.
STRINGi9606.ENSP00000273062.

Structurei

Secondary structure

1
261
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi85 – 873Combined sources
Beta strandi92 – 954Combined sources
Turni99 – 1013Combined sources
Beta strandi102 – 1076Combined sources
Beta strandi113 – 1208Combined sources
Beta strandi123 – 1319Combined sources
Helixi135 – 14511Combined sources
Beta strandi146 – 1516Combined sources
Helixi156 – 16611Combined sources
Beta strandi172 – 1765Combined sources
Helixi178 – 1803Combined sources
Beta strandi181 – 1844Combined sources
Beta strandi187 – 1893Combined sources
Helixi192 – 1943Combined sources
Beta strandi195 – 1973Combined sources
Helixi199 – 2013Combined sources
Beta strandi202 – 2054Combined sources
Helixi209 – 2124Combined sources
Helixi216 – 2183Combined sources
Beta strandi219 – 2213Combined sources
Helixi233 – 24412Combined sources
Helixi251 – 2544Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ9GZU7.
SMRiQ9GZU7. Positions 77-256.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9GZU7.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini86 – 244159FCP1 homologyPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 FCP1 homology domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5190.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiQ9GZU7.
KOiK15731.
OrthoDBiEOG71P2C3.
PhylomeDBiQ9GZU7.
TreeFamiTF313556.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR011948. Dullard_phosphatase.
IPR023214. HAD-like_dom.
IPR004274. NIF.
[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. Align

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 AAP34398.1 differs from that shown. Reason: Frameshift at position 72. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti180 – 1801S → F in BX446444. 1 PublicationCurated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti56 – 561A → T.
Corresponds to variant rs2227249 [ dbSNP | Ensembl ].
VAR_049054

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2222MDSSA…PLRGK → MVAAPWATQEQEEGRGIQPG DR in isoform 3. 1 PublicationVSP_045865Add
BLAST
Alternative sequencei73 – 731Missing in isoform 2 and isoform 3. 2 PublicationsVSP_045866

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]
uc002vhz.3. human. [Q9GZU7-2]

Polymorphism databases

DMDMi17865510.

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 .
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 ]
UniGenei Hs.444468.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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 [» ]
ProteinModelPortali Q9GZU7.
SMRi Q9GZU7. Positions 77-256.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 121804. 14 interactions.
IntActi Q9GZU7. 2 interactions.
MINTi MINT-1441843.
STRINGi 9606.ENSP00000273062.

Chemistry

BindingDBi Q9GZU7.
ChEMBLi CHEMBL1795098.

PTM databases

PhosphoSitei Q9GZU7.

Polymorphism databases

DMDMi 17865510.

Proteomic databases

MaxQBi Q9GZU7.
PaxDbi Q9GZU7.
PRIDEi Q9GZU7.

Protocols and materials databases

DNASUi 58190.
Structural Biology Knowledgebase Search...

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 ]
uc002vhz.3. human. [Q9GZU7-2 ]

Organism-specific databases

CTDi 58190.
GeneCardsi GC02P219262.
HGNCi HGNC:21614. CTDSP1.
MIMi 605323. gene.
neXtProti NX_Q9GZU7.
PharmGKBi PA134938848.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG5190.
GeneTreei ENSGT00390000017194.
HOGENOMi HOG000236379.
HOVERGENi HBG053298.
InParanoidi Q9GZU7.
KOi K15731.
OrthoDBi EOG71P2C3.
PhylomeDBi Q9GZU7.
TreeFami TF313556.

Enzyme and pathway databases

SignaLinki Q9GZU7.

Miscellaneous databases

ChiTaRSi CTDSP1. human.
EvolutionaryTracei Q9GZU7.
GeneWikii CTDSP1.
GenomeRNAii 58190.
NextBioi 64884.
PROi Q9GZU7.
SOURCEi Search...

Gene expression databases

Bgeei Q9GZU7.
CleanExi HS_CTDSP1.
Genevestigatori Q9GZU7.

Family and domain databases

Gene3Di 3.40.50.1000. 1 hit.
InterProi IPR011948. Dullard_phosphatase.
IPR023214. HAD-like_dom.
IPR004274. NIF.
[Graphical view ]
Pfami PF03031. NIF. 1 hit.
[Graphical view ]
SMARTi SM00577. CPDc. 1 hit.
[Graphical view ]
SUPFAMi SSF56784. SSF56784. 1 hit.
TIGRFAMsi TIGR02251. HIF-SF_euk. 1 hit.
PROSITEi PS50969. FCP1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence and genomic structure of the human NRAMP1 gene region on chromosome region 2q35."
    Marquet S., Lepage P., Hudson T.J., Musser J.M., Schurr E.
    Mamm. Genome 11:755-762(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 1).
  2. "A novel RNA polymerase II C-terminal domain phosphatase that preferentially dephosphorylates serine 5."
    Yeo M., Lin P.S., Dahmus M.E., Gill G.N.
    J. Biol. Chem. 278:26078-26085(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [MRNA] OF 50-260 (ISOFORM 2), FUNCTION, SUBCELLULAR LOCATION, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH GTF2F1, MUTAGENESIS OF ASP-96 AND ASP-98.
  3. "Full-length cDNA libraries and normalization."
    Li W.B., Gruber C., Jessee J., Polayes D.
    Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Tissue: Placenta.
  4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Lymph.
  6. "Small CTD phosphatases function in silencing neuronal gene expression."
    Yeo M., Lee S.-K., Lee B., Ruiz E.C., Pfaff S.L., Gill G.N.
    Science 307:596-600(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH REST.
  7. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Structure and mechanism of RNA polymerase II CTD phosphatases."
    Kamenski T., Heilmeier S., Meinhart A., Cramer P.
    Mol. Cell 15:399-407(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 77-261 IN COMPLEX WITH MAGNESIUM AND INHIBITOR.
  9. "Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1."
    Zhang Y., Kim Y., Genoud N., Gao J., Kelly J.W., Pfaff S.L., Gill G.N., Dixon J.E., Noel J.P.
    Mol. Cell 24:759-770(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 77-256 OF MUTANT ASN-96 IN COMPLEX WITH SUBSTRATE PEPTIDES, SUBSTRATE SPECIFICITY.

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 26, 2014
This is version 121 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

External Data

Dasty 3