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Protein

Glycerophosphocholine phosphodiesterase GPCPD1

Gene

GPCPD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.By similarity

Catalytic activityi

sn-glycero-3-phosphocholine + H2O = choline + sn-glycerol 3-phosphate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei70SubstrateSequence analysis1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

BioCyciZFISH:HS04929-MONOMER.
ReactomeiR-HSA-1483115. Hydrolysis of LPC.
R-HSA-1483152. Hydrolysis of LPE.

Protein family/group databases

CAZyiCBM20. Carbohydrate-Binding Module Family 20.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphocholine phosphodiesterase GPCPD1 (EC:3.1.4.2)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 5
Gene namesi
Name:GPCPD1
Synonyms:GDE5, KIAA1434
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

HGNCiHGNC:26957. GPCPD1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi56261.
OpenTargetsiENSG00000125772.
PharmGKBiPA165392351.

Polymorphism and mutation databases

BioMutaiGPCPD1.
DMDMi23821811.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000507971 – 672Glycerophosphocholine phosphodiesterase GPCPD1Add BLAST672

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei175PhosphoserineCombined sources1
Modified residuei424PhosphoserineBy similarity1
Modified residuei608PhosphotyrosineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9NPB8.
MaxQBiQ9NPB8.
PaxDbiQ9NPB8.
PeptideAtlasiQ9NPB8.
PRIDEiQ9NPB8.

PTM databases

iPTMnetiQ9NPB8.
PhosphoSitePlusiQ9NPB8.

Expressioni

Tissue specificityi

Widely expressed, with highest expression in spinal chord.

Gene expression databases

BgeeiENSG00000125772.
ExpressionAtlasiQ9NPB8. baseline and differential.
GenevisibleiQ9NPB8. HS.

Organism-specific databases

HPAiHPA039556.
HPA042987.

Interactioni

Protein-protein interaction databases

BioGridi121125. 2 interactors.
IntActiQ9NPB8. 1 interactor.
MINTiMINT-4650772.
STRINGi9606.ENSP00000368305.

Structurei

Secondary structure

1672
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Beta strandi19 – 26Combined sources8
Helixi27 – 29Combined sources3
Turni30 – 32Combined sources3
Helixi34 – 36Combined sources3
Beta strandi49 – 58Combined sources10
Beta strandi64 – 74Combined sources11
Beta strandi84 – 90Combined sources7
Beta strandi97 – 99Combined sources3
Beta strandi103 – 112Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Z0BX-ray2.00A/B/C/D/E/F3-120[»]
ProteinModelPortaliQ9NPB8.
SMRiQ9NPB8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NPB8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 115CBM20PROSITE-ProRule annotationAdd BLAST115
Domaini318 – 618GP-PDEAdd BLAST301

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni88 – 89Substrate bindingSequence analysis2

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi169 – 172Poly-Asp4

Sequence similaritiesi

Contains 1 CBM20 (carbohydrate binding type-20) domain.PROSITE-ProRule annotation
Contains 1 GP-PDE domain.Curated

Phylogenomic databases

eggNOGiKOG2421. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00440000033970.
HOGENOMiHOG000231653.
HOVERGENiHBG080384.
InParanoidiQ9NPB8.
KOiK18695.
OMAiCGEPDIH.
OrthoDBiEOG091G02LR.
PhylomeDBiQ9NPB8.
TreeFamiTF314722.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.20.20.190. 1 hit.
InterProiIPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR030395. GP_PDE_dom.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PfamiPF00686. CBM_20. 1 hit.
PF03009. GDPD. 1 hit.
[Graphical view]
SMARTiSM01065. CBM_2. 1 hit.
[Graphical view]
SUPFAMiSSF49452. SSF49452. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEiPS51166. CBM20. 1 hit.
PS51704. GP_PDE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9NPB8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPSQVAFEI RGTLLPGEVF AICGSCDALG NWNPQNAVAL LPENDTGESM
60 70 80 90 100
LWKATIVLSR GVSVQYRYFK GYFLEPKTIG GPCQVIVHKW ETHLQPRSIT
110 120 130 140 150
PLESEIIIDD GQFGIHNGVE TLDSGWLTCQ TEIRLRLHYS EKPPVSITKK
160 170 180 190 200
KLKKSRFRVK LTLEGLEEDD DDRVSPTVLH KMSNSLEISL ISDNEFKCRH
210 220 230 240 250
SQPECGYGLQ PDRWTEYSIQ TMEPDNLELI FDFFEEDLSE HVVQGDALPG
260 270 280 290 300
HVGTACLLSS TIAESGKSAG ILTLPIMSRN SRKTIGKVRV DYIIIKPLPG
310 320 330 340 350
YSCDMKSSFS KYWKPRIPLD VGHRGAGNST TTAQLAKVQE NTIASLRNAA
360 370 380 390 400
SHGAAFVEFD VHLSKDFVPV VYHDLTCCLT MKKKFDADPV ELFEIPVKEL
410 420 430 440 450
TFDQLQLLKL THVTALKSKD RKESVVQEEN SFSENQPFPS LKMVLESLPE
460 470 480 490 500
DVGFNIEIKW ICQQRDGMWD GNLSTYFDMN LFLDIILKTV LENSGKRRIV
510 520 530 540 550
FSSFDADICT MVRQKQNKYP ILFLTQGKSE IYPELMDLRS RTTPIAMSFA
560 570 580 590 600
QFENLLGINV HTEDLLRNPS YIQEAKAKGL VIFCWGDDTN DPENRRKLKE
610 620 630 640 650
LGVNGLIYDR IYDWMPEQPN IFQVEQLERL KQELPELKSC LCPTVSRFVP
660 670
SSLCGESDIH VDANGIDNVE NA
Length:672
Mass (Da):76,035
Last modified:October 10, 2002 - v2
Checksum:i9AA17024D231AD74
GO

Sequence cautioni

The sequence BAA91994 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA92672 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_022060273T → I.Corresponds to variant rs2273373dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB037855 mRNA. Translation: BAA92672.1. Different initiation.
AL109935 Genomic DNA. Translation: CAB91047.2.
CH471133 Genomic DNA. Translation: EAX10414.1.
CH471133 Genomic DNA. Translation: EAX10415.1.
BC027588 mRNA. Translation: AAH27588.1.
AK001947 mRNA. Translation: BAA91994.1. Different initiation.
CCDSiCCDS13090.1.
RefSeqiNP_062539.1. NM_019593.3.
XP_005260815.1. XM_005260758.4.
XP_006723659.1. XM_006723596.3.
UniGeneiHs.636359.

Genome annotation databases

EnsembliENST00000379019; ENSP00000368305; ENSG00000125772.
GeneIDi56261.
KEGGihsa:56261.
UCSCiuc002wme.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB037855 mRNA. Translation: BAA92672.1. Different initiation.
AL109935 Genomic DNA. Translation: CAB91047.2.
CH471133 Genomic DNA. Translation: EAX10414.1.
CH471133 Genomic DNA. Translation: EAX10415.1.
BC027588 mRNA. Translation: AAH27588.1.
AK001947 mRNA. Translation: BAA91994.1. Different initiation.
CCDSiCCDS13090.1.
RefSeqiNP_062539.1. NM_019593.3.
XP_005260815.1. XM_005260758.4.
XP_006723659.1. XM_006723596.3.
UniGeneiHs.636359.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Z0BX-ray2.00A/B/C/D/E/F3-120[»]
ProteinModelPortaliQ9NPB8.
SMRiQ9NPB8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121125. 2 interactors.
IntActiQ9NPB8. 1 interactor.
MINTiMINT-4650772.
STRINGi9606.ENSP00000368305.

Protein family/group databases

CAZyiCBM20. Carbohydrate-Binding Module Family 20.

PTM databases

iPTMnetiQ9NPB8.
PhosphoSitePlusiQ9NPB8.

Polymorphism and mutation databases

BioMutaiGPCPD1.
DMDMi23821811.

Proteomic databases

EPDiQ9NPB8.
MaxQBiQ9NPB8.
PaxDbiQ9NPB8.
PeptideAtlasiQ9NPB8.
PRIDEiQ9NPB8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000379019; ENSP00000368305; ENSG00000125772.
GeneIDi56261.
KEGGihsa:56261.
UCSCiuc002wme.5. human.

Organism-specific databases

CTDi56261.
DisGeNETi56261.
GeneCardsiGPCPD1.
HGNCiHGNC:26957. GPCPD1.
HPAiHPA039556.
HPA042987.
MIMi614124. gene.
neXtProtiNX_Q9NPB8.
OpenTargetsiENSG00000125772.
PharmGKBiPA165392351.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2421. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00440000033970.
HOGENOMiHOG000231653.
HOVERGENiHBG080384.
InParanoidiQ9NPB8.
KOiK18695.
OMAiCGEPDIH.
OrthoDBiEOG091G02LR.
PhylomeDBiQ9NPB8.
TreeFamiTF314722.

Enzyme and pathway databases

BioCyciZFISH:HS04929-MONOMER.
ReactomeiR-HSA-1483115. Hydrolysis of LPC.
R-HSA-1483152. Hydrolysis of LPE.

Miscellaneous databases

ChiTaRSiGPCPD1. human.
EvolutionaryTraceiQ9NPB8.
GenomeRNAii56261.
PROiQ9NPB8.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000125772.
ExpressionAtlasiQ9NPB8. baseline and differential.
GenevisibleiQ9NPB8. HS.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.20.20.190. 1 hit.
InterProiIPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR030395. GP_PDE_dom.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PfamiPF00686. CBM_20. 1 hit.
PF03009. GDPD. 1 hit.
[Graphical view]
SMARTiSM01065. CBM_2. 1 hit.
[Graphical view]
SUPFAMiSSF49452. SSF49452. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEiPS51166. CBM20. 1 hit.
PS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGPCP1_HUMAN
AccessioniPrimary (citable) accession number: Q9NPB8
Secondary accession number(s): D3DW06, Q9BQL8, Q9NUX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 10, 2002
Last modified: November 2, 2016
This is version 136 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 20
    Human chromosome 20: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.