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P49585

- PCY1A_HUMAN

UniProt

P49585 - PCY1A_HUMAN

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Protein

Choline-phosphate cytidylyltransferase A

Gene

PCYT1A

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

Functioni

Controls phosphatidylcholine synthesis.

Catalytic activityi

CTP + phosphocholine = diphosphate + CDP-choline.

Enzyme regulationi

By phosphorylation.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei122 – 1221CTPBy similarity
Binding sitei122 – 1221SubstrateBy similarity
Binding sitei151 – 1511SubstrateBy similarity
Binding sitei173 – 1731CTPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi84 – 929CTPBy similarity
Nucleotide bindingi168 – 1692CTPBy similarity
Nucleotide bindingi196 – 2005CTPBy similarity

GO - Molecular functioni

  1. choline-phosphate cytidylyltransferase activity Source: UniProtKB
  2. lipid binding Source: Ensembl

GO - Biological processi

  1. CDP-choline pathway Source: UniProtKB
  2. glycerophospholipid biosynthetic process Source: Reactome
  3. phosphatidylcholine biosynthetic process Source: UniProtKB
  4. phospholipid metabolic process Source: Reactome
  5. small molecule metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Lipid biosynthesis, Lipid metabolism, Phospholipid biosynthesis, Phospholipid metabolism

Enzyme and pathway databases

ReactomeiREACT_121238. Synthesis of PC.
UniPathwayiUPA00753; UER00739.

Names & Taxonomyi

Protein namesi
Recommended name:
Choline-phosphate cytidylyltransferase A (EC:2.7.7.15)
Alternative name(s):
CCT-alpha
CTP:phosphocholine cytidylyltransferase A
Short name:
CCT A
Short name:
CT A
Phosphorylcholine transferase A
Gene namesi
Name:PCYT1A
Synonyms:CTPCT, PCYT1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 3

Organism-specific databases

HGNCiHGNC:8754. PCYT1A.

Subcellular locationi

Cytoplasmcytosol By similarity. Membrane By similarity; Peripheral membrane protein By similarity
Note: It can interconvert between an inactive cytosolic form and an active membrane-bound form.By similarity

GO - Cellular componenti

  1. endoplasmic reticulum membrane Source: UniProtKB
  2. glycogen granule Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Involvement in diseasei

Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940]: A disorder characterized by postnatal growth deficiency resulting in profound short stature, rhizomelia with bowing of the lower extremities, platyspondyly with anterior vertebral protrusions, progressive metaphyseal irregularity and cupping with shortened tubular bones, and early-onset progressive visual impairment associated with a pigmentary maculopathy and electroretinographic evidence of cone-rod dysfunction.2 Publications
Note: The disease is caused by mutations affecting the gene represented in this entry.
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti99 – 991A → T in SMDCRD. 1 Publication
VAR_071083
Natural varianti99 – 991A → V in SMDCRD. 1 Publication
VAR_071084
Natural varianti129 – 1291E → K in SMDCRD. 2 Publications
VAR_071085
Natural varianti150 – 1501P → A in SMDCRD. 1 Publication
VAR_071086
Natural varianti191 – 1911F → L in SMDCRD. 1 Publication
VAR_071087
Natural varianti223 – 2231R → S in SMDCRD. 1 Publication
VAR_071088

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi37 – 371C → S: Abolishes formation of the interchain disulfide that can be observed when the enzyme is treated with copper phenanthrolene (in vitro). 1 Publication

Keywords - Diseasei

Cone-rod dystrophy, Disease mutation, Dwarfism

Organism-specific databases

MIMi608940. phenotype.
Orphaneti85167. Spondylometaphyseal dysplasia - cone-rod dystrophy.
PharmGKBiPA33099.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 367367Choline-phosphate cytidylyltransferase APRO_0000208453Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionine2 Publications
Modified residuei8 – 81N6-acetyllysine1 Publication
Modified residuei315 – 3151Phosphoserine1 Publication
Modified residuei319 – 3191Phosphoserine1 Publication
Modified residuei321 – 3211PhosphoserineBy similarity
Modified residuei322 – 3221PhosphoserineBy similarity
Modified residuei323 – 3231PhosphoserineBy similarity
Modified residuei329 – 3291PhosphoserineBy similarity
Modified residuei331 – 3311PhosphoserineBy similarity
Modified residuei333 – 3331PhosphoserineBy similarity
Modified residuei343 – 3431Phosphoserine2 Publications
Modified residuei347 – 3471Phosphoserine2 Publications
Modified residuei352 – 3521Phosphoserine1 Publication
Modified residuei362 – 3621Phosphoserine6 Publications

Post-translational modificationi

The serine residues of the C-terminus are phosphorylated. The inactive soluble form is stabilized by phosphorylation, the active membrane bound form is promoted by anionic lipids or diacylglycerol, and is stabilized by dephosphorylation (By similarity).By similarity
Monoubiquitinated by the SCF(FBXL2) complex, leading to proteasomal degradation.By similarity

Keywords - PTMi

Acetylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP49585.
PaxDbiP49585.
PRIDEiP49585.

PTM databases

PhosphoSiteiP49585.

Miscellaneous databases

PMAP-CutDBP49585.

Expressioni

Gene expression databases

BgeeiP49585.
CleanExiHS_PCYT1A.
ExpressionAtlasiP49585. baseline and differential.
GenevestigatoriP49585.

Organism-specific databases

HPAiHPA035428.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi111157. 8 interactions.
IntActiP49585. 8 interactions.
STRINGi9606.ENSP00000292823.

Structurei

3D structure databases

ProteinModelPortaliP49585.
SMRiP49585. Positions 40-295.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati319 – 32461
Repeati329 – 33352; approximate
Repeati343 – 34863

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni228 – 28760AmphipathicSequence AnalysisAdd
BLAST
Regioni256 – 288333 X 11 AA approximate tandem repeatsAdd
BLAST
Regioni319 – 348303 X repeatsAdd
BLAST

Sequence similaritiesi

Belongs to the cytidylyltransferase family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0615.
GeneTreeiENSGT00390000000269.
HOGENOMiHOG000230945.
HOVERGENiHBG053531.
InParanoidiP49585.
KOiK00968.
PhylomeDBiP49585.
TreeFamiTF106336.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
InterProiIPR004821. Cyt_trans-like.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF01467. CTP_transf_2. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00125. cyt_tran_rel. 1 hit.

Sequencei

Sequence statusi: Complete.

P49585-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MDAQCSAKVN ARKRRKEAPG PNGATEEDGV PSKVQRCAVG LRQPAPFSDE
60 70 80 90 100
IEVDFSKPYV RVTMEEASRG TPCERPVRVY ADGIFDLFHS GHARALMQAK
110 120 130 140 150
NLFPNTYLIV GVCSDELTHN FKGFTVMNEN ERYDAVQHCR YVDEVVRNAP
160 170 180 190 200
WTLTPEFLAE HRIDFVAHDD IPYSSAGSDD VYKHIKEAGM FAPTQRTEGI
210 220 230 240 250
STSDIITRIV RDYDVYARRN LQRGYTAKEL NVSFINEKKY HLQERVDKVK
260 270 280 290 300
KKVKDVEEKS KEFVQKVEEK SIDLIQKWEE KSREFIGSFL EMFGPEGALK
310 320 330 340 350
HMLKEGKGRM LQAISPKQSP SSSPTRERSP SPSFRWPFSG KTSPPCSPAN
360
LSRHKAAAYD ISEDEED
Length:367
Mass (Da):41,731
Last modified:January 15, 2008 - v2
Checksum:i38CE9D5CF2E2AEE2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti251 – 2511K → E in AAA72127. (PubMed:7918629)Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti99 – 991A → T in SMDCRD. 1 Publication
VAR_071083
Natural varianti99 – 991A → V in SMDCRD. 1 Publication
VAR_071084
Natural varianti129 – 1291E → K in SMDCRD. 2 Publications
VAR_071085
Natural varianti150 – 1501P → A in SMDCRD. 1 Publication
VAR_071086
Natural varianti191 – 1911F → L in SMDCRD. 1 Publication
VAR_071087
Natural varianti223 – 2231R → S in SMDCRD. 1 Publication
VAR_071088

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L28957 mRNA. Translation: AAA72127.1.
EU280320 Genomic DNA. Translation: ABX44666.1.
CH471191 Genomic DNA. Translation: EAW53655.1.
CH471191 Genomic DNA. Translation: EAW53662.1.
BC046355 mRNA. Translation: AAH46355.1.
CCDSiCCDS3315.1.
PIRiS50145.
RefSeqiNP_005008.2. NM_005017.2.
UniGeneiHs.135997.
Hs.732774.

Genome annotation databases

EnsembliENST00000292823; ENSP00000292823; ENSG00000161217.
ENST00000431016; ENSP00000394617; ENSG00000161217.
GeneIDi5130.
KEGGihsa:5130.
UCSCiuc003fwg.3. human.

Polymorphism databases

DMDMi166214967.

Cross-referencesi

Web resourcesi

SeattleSNPs

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L28957 mRNA. Translation: AAA72127.1 .
EU280320 Genomic DNA. Translation: ABX44666.1 .
CH471191 Genomic DNA. Translation: EAW53655.1 .
CH471191 Genomic DNA. Translation: EAW53662.1 .
BC046355 mRNA. Translation: AAH46355.1 .
CCDSi CCDS3315.1.
PIRi S50145.
RefSeqi NP_005008.2. NM_005017.2.
UniGenei Hs.135997.
Hs.732774.

3D structure databases

ProteinModelPortali P49585.
SMRi P49585. Positions 40-295.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 111157. 8 interactions.
IntActi P49585. 8 interactions.
STRINGi 9606.ENSP00000292823.

Chemistry

DrugBanki DB00122. Choline.
DB00709. Lamivudine.

PTM databases

PhosphoSitei P49585.

Polymorphism databases

DMDMi 166214967.

Proteomic databases

MaxQBi P49585.
PaxDbi P49585.
PRIDEi P49585.

Protocols and materials databases

DNASUi 5130.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000292823 ; ENSP00000292823 ; ENSG00000161217 .
ENST00000431016 ; ENSP00000394617 ; ENSG00000161217 .
GeneIDi 5130.
KEGGi hsa:5130.
UCSCi uc003fwg.3. human.

Organism-specific databases

CTDi 5130.
GeneCardsi GC03M195941.
H-InvDB HIX0024337.
HGNCi HGNC:8754. PCYT1A.
HPAi HPA035428.
MIMi 123695. gene.
608940. phenotype.
neXtProti NX_P49585.
Orphaneti 85167. Spondylometaphyseal dysplasia - cone-rod dystrophy.
PharmGKBi PA33099.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0615.
GeneTreei ENSGT00390000000269.
HOGENOMi HOG000230945.
HOVERGENi HBG053531.
InParanoidi P49585.
KOi K00968.
PhylomeDBi P49585.
TreeFami TF106336.

Enzyme and pathway databases

UniPathwayi UPA00753 ; UER00739 .
Reactomei REACT_121238. Synthesis of PC.

Miscellaneous databases

GeneWikii PCYT1A.
GenomeRNAii 5130.
NextBioi 19780.
PMAP-CutDB P49585.
PROi P49585.
SOURCEi Search...

Gene expression databases

Bgeei P49585.
CleanExi HS_PCYT1A.
ExpressionAtlasi P49585. baseline and differential.
Genevestigatori P49585.

Family and domain databases

Gene3Di 3.40.50.620. 1 hit.
InterProi IPR004821. Cyt_trans-like.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view ]
Pfami PF01467. CTP_transf_2. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00125. cyt_tran_rel. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Primary structure and expression of a human CTP:phosphocholine cytidylyltransferase."
    Kalmar G.B., Kay R.J., Lachance A.C., Cornell R.B.
    Biochim. Biophys. Acta 1219:328-334(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. SeattleSNPs variation discovery resource
    Submitted (NOV-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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: Brain.
  5. "Membrane-binding amphipathic alpha-helical peptide derived from CTP:phosphocholine cytidylyltransferase."
    Johnson J.E., Cornell R.B.
    Biochemistry 33:4327-4335(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: MECHANISM OF CYTIDYLYLTRANSFERASE ACTIVATION.
  6. "Structure of the membrane binding domain of CTP:phosphocholine cytidylyltransferase."
    Dunne S.J., Cornell R.B., Johnson J.E., Glover N.R., Tracey A.S.
    Biochemistry 35:11975-11984(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: CIRCULAR DICHROISM, STRUCTURE BY NMR OF 236-268 AND 267-288.
  7. "Membrane binding modulates the quaternary structure of CTP:phosphocholine cytidylyltransferase."
    Xie M., Smith J.L., Ding Z., Zhang D., Cornell R.B.
    J. Biol. Chem. 279:28817-28825(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IN VITRO INTERCHAIN DISULFIDE BOND, MUTAGENESIS OF CYS-37.
  8. "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
    Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
    Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  9. "A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
    Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
    Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  10. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-343; SER-347; SER-352 AND SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  11. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
    Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
    Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-315; SER-319; SER-343; SER-347 AND SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Leukemic T-cell.
  13. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1 AND LYS-8, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-362, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  18. "Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy."
    Hoover-Fong J., Sobreira N., Jurgens J., Modaff P., Blout C., Moser A., Kim O.H., Cho T.J., Cho S.Y., Kim S.J., Jin D.K., Kitoh H., Park W.Y., Ling H., Hetrick K.N., Doheny K.F., Valle D., Pauli R.M.
    Am. J. Hum. Genet. 94:105-112(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANTS SMDCRD THR-99; VAL-99; LYS-129; ALA-150; LEU-191 AND SER-223.
  19. Cited for: VARIANT SMDCRD LYS-129.

Entry informationi

Entry nameiPCY1A_HUMAN
AccessioniPrimary (citable) accession number: P49585
Secondary accession number(s): A9LYK9, D3DXB1, Q86Y88
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 15, 2008
Last modified: October 29, 2014
This is version 137 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3