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Protein

Choline-phosphate cytidylyltransferase A

Gene

PCYT1A

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

Functioni

Controls phosphatidylcholine synthesis.

Catalytic activityi

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

Enzyme 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 A (PCYT1A), Choline-phosphate cytidylyltransferase B (PCYT1B)
  2. Cholinephosphotransferase 1 (CHPT1), Choline/ethanolaminephosphotransferase 1 (CEPT1)
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

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Lipid biosynthesis, Lipid metabolism, Phospholipid biosynthesis, Phospholipid metabolism

Enzyme and pathway databases

BioCyciMetaCyc:HS08577-MONOMER.
ZFISH:HS08577-MONOMER.
ReactomeiR-HSA-1483191. Synthesis of PC.
SIGNORiP49585.
UniPathwayiUPA00753; 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

HGNCiHGNC:8754. PCYT1A.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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 rs587777191dbSNPEnsembl.1
Natural variantiVAR_07108499A → V in SMDCRD. 1 PublicationCorresponds to variant rs587777189dbSNPEnsembl.1
Natural variantiVAR_071085129E → K in SMDCRD. 2 PublicationsCorresponds to variant rs587777194dbSNPEnsembl.1
Natural variantiVAR_071086150P → A in SMDCRD. 1 PublicationCorresponds to variant rs587777190dbSNPEnsembl.1
Natural variantiVAR_071087191F → L in SMDCRD. 1 PublicationCorresponds to variant rs587777195dbSNPEnsembl.1
Natural variantiVAR_071088223R → S in SMDCRD. 1 PublicationCorresponds to variant rs540053239dbSNPEnsembl.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.
Orphaneti85167. Spondylometaphyseal dysplasia - cone-rod dystrophy.
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.

PTM databases

iPTMnetiP49585.
PhosphoSitePlusiP49585.

Miscellaneous databases

PMAP-CutDBP49585.

Expressioni

Gene expression databases

BgeeiENSG00000161217.
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

Protein-protein interaction databases

BioGridi111157. 11 interactors.
IntActiP49585. 16 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.
InterProiIPR004821. Cyt_trans-like.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF01467. CTP_transf_like. 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)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 rs587777191dbSNPEnsembl.1
Natural variantiVAR_07108499A → V in SMDCRD. 1 PublicationCorresponds to variant rs587777189dbSNPEnsembl.1
Natural variantiVAR_071085129E → K in SMDCRD. 2 PublicationsCorresponds to variant rs587777194dbSNPEnsembl.1
Natural variantiVAR_071086150P → A in SMDCRD. 1 PublicationCorresponds to variant rs587777190dbSNPEnsembl.1
Natural variantiVAR_071087191F → L in SMDCRD. 1 PublicationCorresponds to variant rs587777195dbSNPEnsembl.1
Natural variantiVAR_071088223R → S in SMDCRD. 1 PublicationCorresponds to variant rs540053239dbSNPEnsembl.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.

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. 11 interactors.
IntActiP49585. 16 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.

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.
GeneCardsiPCYT1A.
H-InvDBHIX0024337.
HGNCiHGNC:8754. PCYT1A.
HPAiHPA035428.
MalaCardsiPCYT1A.
MIMi123695. gene.
608940. phenotype.
neXtProtiNX_P49585.
OpenTargetsiENSG00000161217.
Orphaneti85167. Spondylometaphyseal dysplasia - cone-rod dystrophy.
PharmGKBiPA33099.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2804. Eukaryota.
COG0615. LUCA.
GeneTreeiENSGT00390000000269.
HOGENOMiHOG000230945.
HOVERGENiHBG053531.
InParanoidiP49585.
KOiK00968.
PhylomeDBiP49585.
TreeFamiTF106336.

Enzyme and pathway databases

UniPathwayiUPA00753; UER00739.
BioCyciMetaCyc:HS08577-MONOMER.
ZFISH:HS08577-MONOMER.
ReactomeiR-HSA-1483191. Synthesis of PC.
SIGNORiP49585.

Miscellaneous databases

GeneWikiiPCYT1A.
GenomeRNAii5130.
PMAP-CutDBP49585.
PROiP49585.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000161217.
CleanExiHS_PCYT1A.
ExpressionAtlasiP49585. baseline and differential.
GenevisibleiP49585. HS.

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_like. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 15, 2008
Last modified: November 30, 2016
This is version 155 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

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 one 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.