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Q9GZU7 (CTDS1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:CTDSP1
Synonyms:NIF3, NLIIF, SCP1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length261 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.6

Catalytic activity

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

Cofactor

Binds 1 magnesium ion per monomer.

Enzyme regulation

Stimulated by GTF2F1. Inhibited by beryllofluoride anions. Ref.2

Subunit structure

Monomer By similarity. Interacts with GTF2F1. Interacts with REST. Ref.2 Ref.6

Subcellular location

Nucleus. Note: Colocalizes with RNA polymerase II. Ref.2

Tissue specificity

Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta. Ref.6

Sequence similarities

Contains 1 FCP1 homology domain.

Biophysicochemical properties

pH dependence:

Optimum pH is 5. Ref.2

Sequence caution

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

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Ctdsp1P584662EBI-751587,EBI-7091612From a different organism.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9GZU7-1)

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.
Isoform 2 (identifier: Q9GZU7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     73-73: Missing.
Isoform 3 (identifier: Q9GZU7-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-22: MDSSAVITQISKEEARGPLRGK → MVAAPWATQEQEEGRGIQPGDR
     73-73: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 261261Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1
PRO_0000212572

Regions

Domain86 – 244159FCP1 homology

Sites

Active site9614-aspartylphosphate intermediate
Active site981Proton donor
Metal binding961Magnesium
Metal binding981Magnesium; via carbonyl oxygen
Metal binding2071Magnesium
Site1521Transition state stabilizer
Site1901Transition state stabilizer

Amino acid modifications

Modified residue11N-acetylmethionine Ref.7

Natural variations

Alternative sequence1 – 2222MDSSA…PLRGK → MVAAPWATQEQEEGRGIQPG DR in isoform 3.
VSP_045865
Alternative sequence731Missing in isoform 2 and isoform 3.
VSP_045866
Natural variant561A → T.
Corresponds to variant rs2227249 [ dbSNP | Ensembl ].
VAR_049054

Experimental info

Mutagenesis961D → E: No effect. Completely abolishes phosphatase activity; when associated with N-98. Ref.2
Mutagenesis981D → N: Completely abolishes phosphatase activity; when associated with E-96. Ref.2
Sequence conflict1801S → F in BX446444. Ref.3

Secondary structure

....................................... 261
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 75A430BCA2748FEA

FASTA26129,203
        10         20         30         40         50         60 
MDSSAVITQI SKEEARGPLR GKGDQKSAAS QKPRSRGILH SLFCCVCRDD GEALPAHSGA 

        70         80         90        100        110        120 
PLLVEENGAI PKQTPVQYLL PEAKAQDSDK ICVVIDLDET LVHSSFKPVN NADFIIPVEI 

       130        140        150        160        170        180 
DGVVHQVYVL KRPHVDEFLQ RMGELFECVL FTASLAKYAD PVADLLDKWG AFRARLFRES 

       190        200        210        220        230        240 
CVFHRGNYVK DLSRLGRDLR RVLILDNSPA SYVFHPDNAV PVASWFDNMS DTELHDLLPF 

       250        260 
FEQLSRVDDV YSVLRQPRPG S 

« Hide

Isoform 2 [UniParc].

Checksum: 30B0CCD745F26DBB
Show »

FASTA26029,075
Isoform 3 [UniParc].

Checksum: D7741284DEE4D3B5
Show »

FASTA26029,128

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS2416.1. [Q9GZU7-1]
CCDS56166.1. [Q9GZU7-3]
RefSeqNP_001193807.1. NM_001206878.1. [Q9GZU7-3]
NP_067021.1. NM_021198.2. [Q9GZU7-1]
NP_872580.1. NM_182642.2. [Q9GZU7-2]
UniGeneHs.444468.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalQ9GZU7.
SMRQ9GZU7. Positions 77-256.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid121804. 5 interactions.
IntActQ9GZU7. 2 interactions.
MINTMINT-1441843.
STRING9606.ENSP00000273062.

Chemistry

BindingDBQ9GZU7.
ChEMBLCHEMBL1795098.

PTM databases

PhosphoSiteQ9GZU7.

Polymorphism databases

DMDM17865510.

Proteomic databases

MaxQBQ9GZU7.
PaxDbQ9GZU7.
PRIDEQ9GZU7.

Protocols and materials databases

DNASU58190.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000273062; ENSP00000273062; ENSG00000144579. [Q9GZU7-1]
ENST00000443891; ENSP00000392248; ENSG00000144579. [Q9GZU7-3]
GeneID58190.
KEGGhsa:58190.
UCSCuc002vhy.3. human. [Q9GZU7-1]
uc002vhz.3. human. [Q9GZU7-2]

Organism-specific databases

CTD58190.
GeneCardsGC02P219262.
HGNCHGNC:21614. CTDSP1.
MIM605323. gene.
neXtProtNX_Q9GZU7.
PharmGKBPA134938848.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5190.
HOGENOMHOG000236379.
HOVERGENHBG053298.
InParanoidQ9GZU7.
KOK15731.
OrthoDBEOG71P2C3.
PhylomeDBQ9GZU7.
TreeFamTF313556.

Enzyme and pathway databases

SignaLinkQ9GZU7.

Gene expression databases

BgeeQ9GZU7.
CleanExHS_CTDSP1.
GenevestigatorQ9GZU7.

Family and domain databases

Gene3D3.40.50.1000. 1 hit.
InterProIPR011948. Dullard_phosphatase.
IPR023214. HAD-like_dom.
IPR004274. NIF.
[Graphical view]
PfamPF03031. NIF. 1 hit.
[Graphical view]
SMARTSM00577. CPDc. 1 hit.
[Graphical view]
SUPFAMSSF56784. SSF56784. 1 hit.
TIGRFAMsTIGR02251. HIF-SF_euk. 1 hit.
PROSITEPS50969. FCP1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCTDSP1. human.
EvolutionaryTraceQ9GZU7.
GeneWikiCTDSP1.
GenomeRNAi58190.
NextBio64884.
PROQ9GZU7.
SOURCESearch...

Entry information

Entry nameCTDS1_HUMAN
AccessionPrimary (citable) accession number: Q9GZU7
Secondary accession number(s): C9IYG0, Q7Z5Q3, Q7Z5Q4
Entry history
Integrated into UniProtKB/Swiss-Prot: December 13, 2001
Last sequence update: March 1, 2001
Last modified: July 9, 2014
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM