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Protein

Glycerophosphodiester phosphodiesterase 1

Gene

GDE1

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

Functioni

Has glycerophosphoinositol phosphodiesterase activity. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).By similarity

Catalytic activityi

1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = myo-inositol + sn-glycerol 3-phosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi97MagnesiumSequence analysis1
Metal bindingi99MagnesiumSequence analysis1
Metal bindingi174MagnesiumSequence analysis1

GO - Molecular functioni

GO - Biological processi

  • glycerophospholipid catabolic process Source: Reactome
  • lipid metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS00157-MONOMER.
BRENDAi3.1.4.44. 2681.
ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase 1 (EC:3.1.4.44)
Alternative name(s):
Membrane-interacting protein of RGS16
RGS16-interacting membrane protein
Gene namesi
Name:GDE1
Synonyms:MIR16
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:29644. GDE1.

Subcellular locationi

  • Cell membrane By similarity; Multi-pass membrane protein Sequence analysis
  • Cytoplasmic vesicle membrane By similarity; Multi-pass membrane protein Sequence analysis

  • Note: Perinuclear vesicles and cell membrane.By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 3CytoplasmicSequence analysis3
Transmembranei4 – 24HelicalSequence analysisAdd BLAST21
Topological domaini25 – 247LumenalSequence analysisAdd BLAST223
Transmembranei248 – 268HelicalSequence analysisAdd BLAST21
Topological domaini269 – 331CytoplasmicSequence analysisAdd BLAST63

GO - Cellular componenti

  • cytoplasmic vesicle membrane Source: UniProtKB-SubCell
  • integral component of membrane Source: UniProtKB
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi51573.
OpenTargetsiENSG00000006007.
PharmGKBiPA162389327.

Polymorphism and mutation databases

BioMutaiGDE1.
DMDMi74734724.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002519441 – 331Glycerophosphodiester phosphodiesterase 1Add BLAST331

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi168N-linked (GlcNAc...)Sequence analysis1
Glycosylationi198N-linked (GlcNAc...)Sequence analysis1

Post-translational modificationi

N-glycosylated.By similarity

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9NZC3.
MaxQBiQ9NZC3.
PaxDbiQ9NZC3.
PeptideAtlasiQ9NZC3.
PRIDEiQ9NZC3.

PTM databases

PhosphoSitePlusiQ9NZC3.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiENSG00000006007.
CleanExiHS_GDE1.
ExpressionAtlasiQ9NZC3. baseline and differential.
GenevisibleiQ9NZC3. HS.

Organism-specific databases

HPAiHPA074747.

Interactioni

Subunit structurei

Interacts with RGS16 (By similarity). Interacts with PRAF2.By similarity1 Publication

Protein-protein interaction databases

BioGridi119618. 18 interactors.
IntActiQ9NZC3. 3 interactors.
STRINGi9606.ENSP00000261386.

Structurei

3D structure databases

ProteinModelPortaliQ9NZC3.
SMRiQ9NZC3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini65 – 331GP-PDEAdd BLAST267

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000047820.
HOGENOMiHOG000006722.
HOVERGENiHBG052946.
InParanoidiQ9NZC3.
KOiK19179.
OMAiINFHIAD.
OrthoDBiEOG091G0ALO.
PhylomeDBiQ9NZC3.
TreeFamiTF313692.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9NZC3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MWLWEDQGGL LGPFSFLLLV LLLVTRSPVN ACLLTGSLFV LLRVFSFEPV
60 70 80 90 100
PSCRALQVLK PRDRISAIAH RGGSHDAPEN TLAAIRQAAK NGATGVELDI
110 120 130 140 150
EFTSDGIPVL MHDNTVDRTT DGTGRLCDLT FEQIRKLNPA ANHRLRNDFP
160 170 180 190 200
DEKIPTLREA VAECLNHNLT IFFDVKGHAH KATEALKKMY MEFPQLYNNS
210 220 230 240 250
VVCSFLPEVI YKMRQTDRDV ITALTHRPWS LSHTGDGKPR YDTFWKHFIF
260 270 280 290 300
VMMDILLDWS MHNILWYLCG ISAFLMQKDF VSPAYLKKWS AKGIQVVGWT
310 320 330
VNTFDEKSYY ESHLGSSYIT DSMVEDCEPH F
Length:331
Mass (Da):37,718
Last modified:October 1, 2000 - v1
Checksum:iEFE567E71DBD4AC5
GO

Sequence cautioni

The sequence AAC05440 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence AAC05803 differs from that shown. Reason: Erroneous gene model prediction.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_044018218R → Q.Corresponds to variant rs2072086dbSNPEnsembl.1
Natural variantiVAR_044019328E → K.Corresponds to variant rs34137361dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212862 mRNA. Translation: AAF65234.1.
AY463154 mRNA. Translation: AAR25624.1.
U91321 Genomic DNA. Translation: AAC05440.1. Sequence problems.
AC003108 Genomic DNA. Translation: AAC05803.1. Sequence problems.
BC014981 mRNA. Translation: AAH14981.1.
BC025273 mRNA. Translation: AAH25273.1.
CCDSiCCDS10578.1.
PIRiT01371.
RefSeqiNP_057725.1. NM_016641.3.
UniGeneiHs.512607.

Genome annotation databases

EnsembliENST00000353258; ENSP00000261386; ENSG00000006007.
GeneIDi51573.
KEGGihsa:51573.
UCSCiuc002dgh.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212862 mRNA. Translation: AAF65234.1.
AY463154 mRNA. Translation: AAR25624.1.
U91321 Genomic DNA. Translation: AAC05440.1. Sequence problems.
AC003108 Genomic DNA. Translation: AAC05803.1. Sequence problems.
BC014981 mRNA. Translation: AAH14981.1.
BC025273 mRNA. Translation: AAH25273.1.
CCDSiCCDS10578.1.
PIRiT01371.
RefSeqiNP_057725.1. NM_016641.3.
UniGeneiHs.512607.

3D structure databases

ProteinModelPortaliQ9NZC3.
SMRiQ9NZC3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119618. 18 interactors.
IntActiQ9NZC3. 3 interactors.
STRINGi9606.ENSP00000261386.

PTM databases

PhosphoSitePlusiQ9NZC3.

Polymorphism and mutation databases

BioMutaiGDE1.
DMDMi74734724.

Proteomic databases

EPDiQ9NZC3.
MaxQBiQ9NZC3.
PaxDbiQ9NZC3.
PeptideAtlasiQ9NZC3.
PRIDEiQ9NZC3.

Protocols and materials databases

DNASUi51573.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000353258; ENSP00000261386; ENSG00000006007.
GeneIDi51573.
KEGGihsa:51573.
UCSCiuc002dgh.4. human.

Organism-specific databases

CTDi51573.
DisGeNETi51573.
GeneCardsiGDE1.
HGNCiHGNC:29644. GDE1.
HPAiHPA074747.
MIMi605943. gene.
neXtProtiNX_Q9NZC3.
OpenTargetsiENSG00000006007.
PharmGKBiPA162389327.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000047820.
HOGENOMiHOG000006722.
HOVERGENiHBG052946.
InParanoidiQ9NZC3.
KOiK19179.
OMAiINFHIAD.
OrthoDBiEOG091G0ALO.
PhylomeDBiQ9NZC3.
TreeFamiTF313692.

Enzyme and pathway databases

BioCyciZFISH:HS00157-MONOMER.
BRENDAi3.1.4.44. 2681.
ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Miscellaneous databases

ChiTaRSiGDE1. human.
GenomeRNAii51573.
PROiQ9NZC3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000006007.
CleanExiHS_GDE1.
ExpressionAtlasiQ9NZC3. baseline and differential.
GenevisibleiQ9NZC3. HS.

Family and domain databases

Gene3Di3.20.20.190. 1 hit.
InterProiIPR004129. GlyceroP-diester-Pdiesterase.
IPR030395. GP_PDE_dom.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERiPTHR23344. PTHR23344. 1 hit.
PfamiPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMiSSF51695. SSF51695. 1 hit.
PROSITEiPS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGDE1_HUMAN
AccessioniPrimary (citable) accession number: Q9NZC3
Secondary accession number(s): O43334, Q6PKF7, Q7KYR4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 118 of the entry and version 1 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 16
    Human chromosome 16: 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. 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.