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Protein

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2

Gene

CTDSP2

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. May contribute to the development of sarcomas.2 Publications

Catalytic activityi

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

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei107 – 10714-aspartylphosphate intermediateBy similarity
Metal bindingi107 – 1071Magnesium1 Publication
Active sitei109 – 1091Proton donorBy similarity
Metal bindingi109 – 1091Magnesium; via carbonyl oxygen1 Publication
Sitei163 – 1631Transition state stabilizerBy similarity
Sitei201 – 2011Transition state stabilizerBy similarity
Metal bindingi218 – 2181Magnesium1 Publication

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

ReactomeiREACT_18273. XBP1(S) activates chaperone genes.
SignaLinkiO14595.

Names & Taxonomyi

Protein namesi
Recommended name:
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 (EC:3.1.3.16)
Alternative name(s):
Nuclear LIM interactor-interacting factor 2
Short name:
NLI-interacting factor 2
Protein OS-4
Small C-terminal domain phosphatase 2
Small CTD phosphatase 2
Short name:
SCP2
Gene namesi
Name:CTDSP2
Synonyms:NIF2, OS4, SCP2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:17077. CTDSP2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA128394568.

Polymorphism and mutation databases

BioMutaiCTDSP2.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 271271Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2PRO_0000212574Add
BLAST

Proteomic databases

MaxQBiO14595.
PaxDbiO14595.
PRIDEiO14595.

PTM databases

DEPODiO14595.
PhosphoSiteiO14595.

Expressioni

Tissue specificityi

Expression is restricted to non-neuronal tissues. Highest expression in pancreas and lowest in liver.1 Publication

Inductioni

In primary sarcomas.

Gene expression databases

BgeeiO14595.
CleanExiHS_CTDSP2.
HS_SCP2.
ExpressionAtlasiO14595. baseline and differential.
GenevisibleiO14595. HS.

Organism-specific databases

HPAiHPA052607.

Interactioni

Subunit structurei

Monomer (By similarity). Interacts with REST.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ARP102753EBI-2802973,EBI-608057
CDCA3Q996185EBI-2802973,EBI-739534
taxP140793EBI-2802973,EBI-9675698From a different organism.

Protein-protein interaction databases

BioGridi115412. 21 interactions.
DIPiDIP-61245N.
IntActiO14595. 7 interactions.
MINTiMINT-2735588.
STRINGi9606.ENSP00000381148.

Structurei

Secondary structure

1
271
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni96 – 1005Combined sources
Beta strandi103 – 1064Combined sources
Turni110 – 1123Combined sources
Beta strandi113 – 1186Combined sources
Beta strandi124 – 1318Combined sources
Beta strandi134 – 1429Combined sources
Helixi146 – 15611Combined sources
Beta strandi157 – 1626Combined sources
Helixi167 – 17711Combined sources
Beta strandi183 – 1875Combined sources
Helixi189 – 1913Combined sources
Beta strandi192 – 1954Combined sources
Beta strandi198 – 2003Combined sources
Helixi203 – 2053Combined sources
Beta strandi206 – 2083Combined sources
Helixi210 – 2123Combined sources
Beta strandi213 – 2186Combined sources
Helixi220 – 2234Combined sources
Helixi227 – 2293Combined sources
Beta strandi230 – 2323Combined sources
Helixi244 – 25512Combined sources
Helixi261 – 2688Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q5EX-ray2.51A/B/C/D/E/F/G/H87-271[»]
ProteinModelPortaliO14595.
SMRiO14595. Positions 90-270.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO14595.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini97 – 255159FCP1 homologyPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 FCP1 homology domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5190.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiO14595.
KOiK15731.
OrthoDBiEOG71P2C3.
PhylomeDBiO14595.
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]

Sequencei

Sequence statusi: Complete.

O14595-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEHGSIITQA RREDALVLTK QGLVSKSSPK KPRGRNIFKA LFCCFRAQHV
60 70 80 90 100
GQSSSSTELA AYKEEANTIA KSDLLQCLQY QFYQIPGTCL LPEVTEEDQG
110 120 130 140 150
RICVVIDLDE TLVHSSFKPI NNADFIVPIE IEGTTHQVYV LKRPYVDEFL
160 170 180 190 200
RRMGELFECV LFTASLAKYA DPVTDLLDRC GVFRARLFRE SCVFHQGCYV
210 220 230 240 250
KDLSRLGRDL RKTLILDNSP ASYIFHPENA VPVQSWFDDM ADTELLNLIP
260 270
IFEELSGAED VYTSLGQLRA P
Length:271
Mass (Da):30,664
Last modified:November 9, 2004 - v2
Checksum:iE4FA4A1657F2B03F
GO

Sequence cautioni

The sequence AAB71816.1 differs from that shown. Reason: Frameshift at position 267. Curated
The sequence AAP34399.1 differs from that shown. Reason: Frameshift at position 267. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti9 – 91Q → H in AAD09331 (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000152 mRNA. Translation: AAB71816.1. Frameshift.
AY279531 mRNA. Translation: AAP34399.1. Frameshift.
AF022231 mRNA. Translation: AAD09331.1.
AK291289 mRNA. Translation: BAF83978.1.
CH471054 Genomic DNA. Translation: EAW97083.1.
BC065920 mRNA. Translation: AAH65920.1.
CCDSiCCDS41801.1.
RefSeqiNP_005721.3. NM_005730.3.
UniGeneiHs.524530.

Genome annotation databases

EnsembliENST00000398073; ENSP00000381148; ENSG00000175215.
GeneIDi10106.
KEGGihsa:10106.
UCSCiuc001sqm.3. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000152 mRNA. Translation: AAB71816.1. Frameshift.
AY279531 mRNA. Translation: AAP34399.1. Frameshift.
AF022231 mRNA. Translation: AAD09331.1.
AK291289 mRNA. Translation: BAF83978.1.
CH471054 Genomic DNA. Translation: EAW97083.1.
BC065920 mRNA. Translation: AAH65920.1.
CCDSiCCDS41801.1.
RefSeqiNP_005721.3. NM_005730.3.
UniGeneiHs.524530.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q5EX-ray2.51A/B/C/D/E/F/G/H87-271[»]
ProteinModelPortaliO14595.
SMRiO14595. Positions 90-270.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115412. 21 interactions.
DIPiDIP-61245N.
IntActiO14595. 7 interactions.
MINTiMINT-2735588.
STRINGi9606.ENSP00000381148.

PTM databases

DEPODiO14595.
PhosphoSiteiO14595.

Polymorphism and mutation databases

BioMutaiCTDSP2.

Proteomic databases

MaxQBiO14595.
PaxDbiO14595.
PRIDEiO14595.

Protocols and materials databases

DNASUi10106.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000398073; ENSP00000381148; ENSG00000175215.
GeneIDi10106.
KEGGihsa:10106.
UCSCiuc001sqm.3. human.

Organism-specific databases

CTDi10106.
GeneCardsiGC12M058213.
HGNCiHGNC:17077. CTDSP2.
HPAiHPA052607.
MIMi608711. gene.
neXtProtiNX_O14595.
PharmGKBiPA128394568.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5190.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiO14595.
KOiK15731.
OrthoDBiEOG71P2C3.
PhylomeDBiO14595.
TreeFamiTF313556.

Enzyme and pathway databases

ReactomeiREACT_18273. XBP1(S) activates chaperone genes.
SignaLinkiO14595.

Miscellaneous databases

ChiTaRSiCTDSP2. human.
EvolutionaryTraceiO14595.
GeneWikiiCTDSP2.
GenomeRNAii10106.
NextBioi38225.
PROiO14595.
SOURCEiSearch...

Gene expression databases

BgeeiO14595.
CleanExiHS_CTDSP2.
HS_SCP2.
ExpressionAtlasiO14595. baseline and differential.
GenevisibleiO14595. HS.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of a highly conserved gene (OS4) amplified with CDK4 in human sarcomas."
    Su Y.A., Lee M.M., Hutter C.M., Meltzer P.S.
    Oncogene 15:1289-1294(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  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], FUNCTION.
  3. Morikane K., Hollingsworth M.A.
    Submitted (SEP-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Fetal pancreas.
  4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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].
    Tissue: Leukocyte.
  7. "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.
  8. Cited for: X-RAY CRYSTALLOGRAPHY (2.51 ANGSTROMS) OF 87-271 IN COMPLEX WITH MAGNESIUM.

Entry informationi

Entry nameiCTDS2_HUMAN
AccessioniPrimary (citable) accession number: O14595
Secondary accession number(s): A8K5H4
, Q53ZR2, Q6NZY3, Q9UEX1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 13, 2001
Last sequence update: November 9, 2004
Last modified: July 22, 2015
This is version 126 of the entry and version 2 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 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.