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Protein

Choline-phosphate cytidylyltransferase A

Gene

PCYT1A

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

Functioni

Controls phosphatidylcholine synthesis.

Catalytic activityi

CTP + phosphocholine = diphosphate + CDP-choline.By similarity

Activity regulationi

By phosphorylation.By similarity

Pathwayi: phosphatidylcholine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes phosphatidylcholine from phosphocholine.By similarity
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Choline-phosphate cytidylyltransferase B (PCYT1B), Choline-phosphate cytidylyltransferase A (PCYT1A)
  2. Choline/ethanolaminephosphotransferase 1 (CEPT1), Cholinephosphotransferase 1 (CHPT1)
This subpathway is part of the pathway phosphatidylcholine biosynthesis, which is itself part of Phospholipid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes phosphatidylcholine from phosphocholine, the pathway phosphatidylcholine biosynthesis and in Phospholipid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei122CTPBy similarity1
Binding sitei122SubstrateBy similarity1
Binding sitei151SubstrateBy similarity1
Binding sitei173CTPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi84 – 92CTPBy similarity9
Nucleotide bindingi168 – 169CTPBy similarity2
Nucleotide bindingi196 – 200CTPBy similarity5

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionNucleotidyltransferase, Transferase
Biological processLipid biosynthesis, Lipid metabolism, Phospholipid biosynthesis, Phospholipid metabolism

Enzyme and pathway databases

BioCyciMetaCyc:HS08577-MONOMER
ReactomeiR-HSA-1483191 Synthesis of PC
SIGNORiP49585
UniPathwayi
UPA00753;UER00739

Names & Taxonomyi

Protein namesi
Recommended name:
Choline-phosphate cytidylyltransferase A (EC:2.7.7.15By similarity)
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
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000161217.11
HGNCiHGNC:8754 PCYT1A
MIMi123695 gene
neXtProtiNX_P49585

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Involvement in diseasei

Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA 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.
See also OMIM:608940
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07108399A → T in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777191EnsemblClinVar.1
Natural variantiVAR_07108499A → V in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777189EnsemblClinVar.1
Natural variantiVAR_071085129E → K in SMDCRD. 2 PublicationsCorresponds to variant dbSNP:rs587777194EnsemblClinVar.1
Natural variantiVAR_071086150P → A in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777190EnsemblClinVar.1
Natural variantiVAR_071087191F → L in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777195EnsemblClinVar.1
Natural variantiVAR_071088223R → S in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs540053239EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi37C → S: Abolishes formation of the interchain disulfide that can be observed when the enzyme is treated with copper phenanthrolene (in vitro). 1 Publication1

Keywords - Diseasei

Cone-rod dystrophy, Disease mutation, Dwarfism

Organism-specific databases

DisGeNETi5130
MalaCardsiPCYT1A
MIMi608940 phenotype
OpenTargetsiENSG00000161217
Orphaneti65 Leber congenital amaurosis
85167 Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
PharmGKBiPA33099

Chemistry databases

DrugBankiDB00122 Choline
DB00709 Lamivudine

Polymorphism and mutation databases

BioMutaiPCYT1A
DMDMi166214967

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002084531 – 367Choline-phosphate cytidylyltransferase AAdd BLAST367

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineCombined sources1
Modified residuei8N6-acetyllysineCombined sources1
Modified residuei233PhosphoserineCombined sources1
Modified residuei315PhosphoserineCombined sources1
Modified residuei319PhosphoserineCombined sources1
Modified residuei321PhosphoserineBy similarity1
Modified residuei322PhosphoserineBy similarity1
Modified residuei323PhosphoserineBy similarity1
Modified residuei325PhosphothreonineBy similarity1
Modified residuei329PhosphoserineBy similarity1
Modified residuei331PhosphoserineCombined sources1
Modified residuei333PhosphoserineBy similarity1
Modified residuei342PhosphothreonineCombined sources1
Modified residuei343PhosphoserineCombined sources1
Modified residuei347PhosphoserineCombined sources1
Modified residuei352PhosphoserineCombined sources1
Modified residuei362PhosphoserineCombined sources1

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

EPDiP49585
MaxQBiP49585
PaxDbiP49585
PeptideAtlasiP49585
PRIDEiP49585
ProteomicsDBi56021

PTM databases

iPTMnetiP49585
PhosphoSitePlusiP49585

Miscellaneous databases

PMAP-CutDBiP49585

Expressioni

Gene expression databases

BgeeiENSG00000161217 Expressed in 209 organ(s), highest expression level in tendon
CleanExiHS_PCYT1A
ExpressionAtlasiP49585 baseline and differential
GenevisibleiP49585 HS

Organism-specific databases

HPAiHPA035428

Interactioni

Subunit structurei

Homodimer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
PCYT1BQ9Y5K3-34EBI-2563309,EBI-12280028

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111157, 12 interactors
IntActiP49585, 25 interactors
STRINGi9606.ENSP00000292823

Structurei

3D structure databases

ProteinModelPortaliP49585
SMRiP49585
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati319 – 32416
Repeati329 – 3332; approximate5
Repeati343 – 34836

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni228 – 287AmphipathicSequence analysisAdd BLAST60
Regioni256 – 2883 X 11 AA approximate tandem repeatsAdd BLAST33
Regioni319 – 3483 X repeatsAdd BLAST30

Sequence similaritiesi

Belongs to the cytidylyltransferase family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2804 Eukaryota
COG0615 LUCA
GeneTreeiENSGT00390000000269
HOGENOMiHOG000230945
HOVERGENiHBG053531
InParanoidiP49585
KOiK00968
PhylomeDBiP49585
TreeFamiTF106336

Family and domain databases

Gene3Di3.40.50.620, 1 hit
InterProiView protein in InterPro
IPR004821 Cyt_trans-like
IPR014729 Rossmann-like_a/b/a_fold
PfamiView protein in Pfam
PF01467 CTP_transf_like, 1 hit
TIGRFAMsiTIGR00125 cyt_tran_rel, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 9 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 9 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9JEJ2C9JEJ2_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
380Annotation score:
C9J050C9J050_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
293Annotation score:
C9JPY0C9JPY0_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
133Annotation score:
C9JVS0C9JVS0_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
115Annotation score:
H7C1T3H7C1T3_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
201Annotation score:
C9J2E1C9J2E1_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
212Annotation score:
F8WAZ5F8WAZ5_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
134Annotation score:
H7BZN1H7BZN1_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
137Annotation score:
F8WBU2F8WBU2_HUMAN
Choline-phosphate cytidylyltransfer...
PCYT1A
90Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti251K → E in AAA72127 (PubMed:7918629).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07108399A → T in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777191EnsemblClinVar.1
Natural variantiVAR_07108499A → V in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777189EnsemblClinVar.1
Natural variantiVAR_071085129E → K in SMDCRD. 2 PublicationsCorresponds to variant dbSNP:rs587777194EnsemblClinVar.1
Natural variantiVAR_071086150P → A in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777190EnsemblClinVar.1
Natural variantiVAR_071087191F → L in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs587777195EnsemblClinVar.1
Natural variantiVAR_071088223R → S in SMDCRD. 1 PublicationCorresponds to variant dbSNP:rs540053239EnsemblClinVar.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001299602.1, NM_001312673.1
NP_005008.2, NM_005017.3
UniGeneiHs.135997
Hs.732774

Genome annotation databases

EnsembliENST00000292823; ENSP00000292823; ENSG00000161217
ENST00000431016; ENSP00000394617; ENSG00000161217
GeneIDi5130
KEGGihsa:5130
UCSCiuc003fwf.2 human

Similar proteinsi

Cross-referencesi

Web resourcesi

SeattleSNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001299602.1, NM_001312673.1
NP_005008.2, NM_005017.3
UniGeneiHs.135997
Hs.732774

3D structure databases

ProteinModelPortaliP49585
SMRiP49585
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111157, 12 interactors
IntActiP49585, 25 interactors
STRINGi9606.ENSP00000292823

Chemistry databases

DrugBankiDB00122 Choline
DB00709 Lamivudine

PTM databases

iPTMnetiP49585
PhosphoSitePlusiP49585

Polymorphism and mutation databases

BioMutaiPCYT1A
DMDMi166214967

Proteomic databases

EPDiP49585
MaxQBiP49585
PaxDbiP49585
PeptideAtlasiP49585
PRIDEiP49585
ProteomicsDBi56021

Protocols and materials databases

DNASUi5130
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000292823; ENSP00000292823; ENSG00000161217
ENST00000431016; ENSP00000394617; ENSG00000161217
GeneIDi5130
KEGGihsa:5130
UCSCiuc003fwf.2 human

Organism-specific databases

CTDi5130
DisGeNETi5130
EuPathDBiHostDB:ENSG00000161217.11
GeneCardsiPCYT1A
H-InvDBiHIX0024337
HGNCiHGNC:8754 PCYT1A
HPAiHPA035428
MalaCardsiPCYT1A
MIMi123695 gene
608940 phenotype
neXtProtiNX_P49585
OpenTargetsiENSG00000161217
Orphaneti65 Leber congenital amaurosis
85167 Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
PharmGKBiPA33099
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2804 Eukaryota
COG0615 LUCA
GeneTreeiENSGT00390000000269
HOGENOMiHOG000230945
HOVERGENiHBG053531
InParanoidiP49585
KOiK00968
PhylomeDBiP49585
TreeFamiTF106336

Enzyme and pathway databases

UniPathwayi
UPA00753;UER00739

BioCyciMetaCyc:HS08577-MONOMER
ReactomeiR-HSA-1483191 Synthesis of PC
SIGNORiP49585

Miscellaneous databases

ChiTaRSiPCYT1A human
GeneWikiiPCYT1A
GenomeRNAii5130
PMAP-CutDBiP49585
PROiPR:P49585
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000161217 Expressed in 209 organ(s), highest expression level in tendon
CleanExiHS_PCYT1A
ExpressionAtlasiP49585 baseline and differential
GenevisibleiP49585 HS

Family and domain databases

Gene3Di3.40.50.620, 1 hit
InterProiView protein in InterPro
IPR004821 Cyt_trans-like
IPR014729 Rossmann-like_a/b/a_fold
PfamiView protein in Pfam
PF01467 CTP_transf_like, 1 hit
TIGRFAMsiTIGR00125 cyt_tran_rel, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPCY1A_HUMAN
AccessioniPrimary (citable) accession number: P49585
Secondary accession number(s): A9LYK9, D3DXB1, Q86Y88
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 15, 2008
Last modified: November 7, 2018
This is version 168 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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Main funding by: National Institutes of Health

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