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Protein

Glycerophosphodiester phosphodiesterase domain-containing protein 3

Gene

GDPD3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi71Divalent metal cationSequence analysis1
Metal bindingi73Divalent metal cationSequence analysis1
Metal bindingi86Divalent metal cationSequence analysis1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase domain-containing protein 3 (EC:3.1.-.-)
Gene namesi
Name:GDPD3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

HGNCiHGNC:28638. GDPD3.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 2CytoplasmicSequence analysis2
Transmembranei3 – 23HelicalSequence analysisAdd BLAST21
Topological domaini24 – 198ExtracellularSequence analysisAdd BLAST175
Transmembranei199 – 221HelicalSequence analysisAdd BLAST23
Topological domaini222 – 318CytoplasmicSequence analysisAdd BLAST97

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Organism-specific databases

DisGeNETi79153.
OpenTargetsiENSG00000102886.
PharmGKBiPA142671741.

Polymorphism and mutation databases

BioMutaiGDPD3.
DMDMi226694188.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002519361 – 318Glycerophosphodiester phosphodiesterase domain-containing protein 3Add BLAST318

Proteomic databases

PaxDbiQ7L5L3.
PeptideAtlasiQ7L5L3.
PRIDEiQ7L5L3.

PTM databases

iPTMnetiQ7L5L3.
PhosphoSitePlusiQ7L5L3.

Expressioni

Gene expression databases

BgeeiENSG00000102886.
CleanExiHS_GDPD3.
ExpressionAtlasiQ7L5L3. baseline and differential.
GenevisibleiQ7L5L3. HS.

Organism-specific databases

HPAiHPA041148.
HPA041470.

Interactioni

Protein-protein interaction databases

BioGridi122571. 6 interactors.
STRINGi9606.ENSP00000384363.

Structurei

3D structure databases

ProteinModelPortaliQ7L5L3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini39 – 308GP-PDEAdd BLAST270

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ7L5L3.
OMAiFLELDCQ.
OrthoDBiEOG091G0G89.
PhylomeDBiQ7L5L3.
TreeFamiTF328545.

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]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q7L5L3-2) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSLLLYYALP ALGSYAMLSI FFLRRPHLLH TPRAPTFRIR LGAHRGGSGE
60 70 80 90 100
LLENTMEAME NSMAQRSDLL ELDCQLTRDR VVVVSHDENL CRQSGLNRDV
110 120 130 140 150
GSLDFEDLPL YKEKLEVYFS PGHFAHGSDR RMVRLEDLFQ RFPRTPMSVE
160 170 180 190 200
IKGKNEELIR EIAGLVRRYD RNEITIWASE KSSVMKKCKA ANPEMPLSFT
210 220 230 240 250
ISRGFWVLLS YYLGLLPFIP IPEKFFFCFL PNIINRTYFP FSCSCLNQLL
260 270 280 290 300
AVVSKWLIMR KSLIRHLEER GVQVVFWCLN EESDFEAAFS VGATGVITDY
310
PTALRHYLDN HGPAARTS
Length:318
Mass (Da):36,596
Last modified:April 14, 2009 - v3
Checksum:i4BD2FF25CF0CA22E
GO
Isoform 2 (identifier: Q7L5L3-1) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-62: Missing.

Show »
Length:256
Mass (Da):29,624
Checksum:i93D3C82D78A7F0CC
GO

Sequence cautioni

The sequence AAH02714 differs from that shown. Reason: Erroneous initiation.Curated

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0368881 – 62Missing in isoform 2. 1 PublicationAdd BLAST62

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026256 mRNA. Translation: BAB15414.1.
AC012645 Genomic DNA. No translation available.
BC002714 mRNA. Translation: AAH02714.2. Different initiation.
CCDSiCCDS10671.2. [Q7L5L3-2]
RefSeqiNP_077283.2. NM_024307.2. [Q7L5L3-2]
UniGeneiHs.289015.

Genome annotation databases

EnsembliENST00000406256; ENSP00000384363; ENSG00000102886. [Q7L5L3-2]
GeneIDi79153.
KEGGihsa:79153.
UCSCiuc002dwp.4. human. [Q7L5L3-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK026256 mRNA. Translation: BAB15414.1.
AC012645 Genomic DNA. No translation available.
BC002714 mRNA. Translation: AAH02714.2. Different initiation.
CCDSiCCDS10671.2. [Q7L5L3-2]
RefSeqiNP_077283.2. NM_024307.2. [Q7L5L3-2]
UniGeneiHs.289015.

3D structure databases

ProteinModelPortaliQ7L5L3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122571. 6 interactors.
STRINGi9606.ENSP00000384363.

PTM databases

iPTMnetiQ7L5L3.
PhosphoSitePlusiQ7L5L3.

Polymorphism and mutation databases

BioMutaiGDPD3.
DMDMi226694188.

Proteomic databases

PaxDbiQ7L5L3.
PeptideAtlasiQ7L5L3.
PRIDEiQ7L5L3.

Protocols and materials databases

DNASUi79153.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000406256; ENSP00000384363; ENSG00000102886. [Q7L5L3-2]
GeneIDi79153.
KEGGihsa:79153.
UCSCiuc002dwp.4. human. [Q7L5L3-2]

Organism-specific databases

CTDi79153.
DisGeNETi79153.
GeneCardsiGDPD3.
HGNCiHGNC:28638. GDPD3.
HPAiHPA041148.
HPA041470.
MIMi616318. gene.
neXtProtiNX_Q7L5L3.
OpenTargetsiENSG00000102886.
PharmGKBiPA142671741.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ7L5L3.
OMAiFLELDCQ.
OrthoDBiEOG091G0G89.
PhylomeDBiQ7L5L3.
TreeFamiTF328545.

Enzyme and pathway databases

ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Miscellaneous databases

GenomeRNAii79153.
PROiQ7L5L3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000102886.
CleanExiHS_GDPD3.
ExpressionAtlasiQ7L5L3. baseline and differential.
GenevisibleiQ7L5L3. 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 nameiGDPD3_HUMAN
AccessioniPrimary (citable) accession number: Q7L5L3
Secondary accession number(s): Q9H652
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: April 14, 2009
Last modified: November 2, 2016
This is version 104 of the entry and version 3 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. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. 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.