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Protein

Lysophospholipase D GDPD1

Gene

GDPD1

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

Functioni

Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine.By similarity

Catalytic activityi

1-alkyl-sn-glycero-3-phosphoethanolamine + H2O = 1-alkyl-sn-glycerol 3-phosphate + ethanolamine.By similarity
1-acyl-sn-glycero-3-phospho-(N-acyl)-ethanolamine + H2O = 1-acyl-sn-glycero-3-phosphate + N-acylethanolamine.By similarity
1-acyl-sn-glycero-3-phosphoethanolamine + H2O = 1-acyl-sn-glycero-3-phosphate + ethanolamine.By similarity
1-O-(alk-1Z-enyl)-sn-glycero-3-phospho-(N-acyl)-ethanolamine + H2O = 1-O-(1Z-alkenyl)-sn-glycero-3-phosphate + N-acylethanolamine.By similarity
1-acyl-sn-glycero-3-phosphocholine + H2O = 1-acyl-sn-glycero-3-phosphate + choline.By similarity
1-O-alkyl-sn-glycero-3-phosphocholine + H2O = 1-O-alkyl-sn-glycero-3-phosphate + choline.By similarity
1-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphate + choline.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi72Divalent metal cationSequence analysis1
Metal bindingi74Divalent metal cationSequence analysis1
Metal bindingi87Divalent metal cationSequence analysis1

GO - Molecular functioni

  • alkylglycerophosphoethanolamine phosphodiesterase activity Source: UniProtKB-EC
  • lysophospholipase activity Source: MGI
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Keywordsi

Molecular functionHydrolase
LigandMetal-binding

Enzyme and pathway databases

BRENDAi3.1.4.46 2681
ReactomeiR-HSA-6814848 Glycerophospholipid catabolism

Chemistry databases

SwissLipidsiSLP:000001718

Names & Taxonomyi

Protein namesi
Recommended name:
Lysophospholipase D GDPD1Curated (EC:3.1.4.39By similarity)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 41 Publication
Glycerophosphodiester phosphodiesterase domain-containing protein 1
Gene namesi
Name:GDPD1Imported
Synonyms:GDE4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

EuPathDBiHostDB:ENSG00000153982.10
HGNCiHGNC:20883 GDPD1
MIMi616317 gene
neXtProtiNX_Q8N9F7

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 3ExtracellularSequence analysis3
Transmembranei4 – 24HelicalSequence analysisAdd BLAST21
Topological domaini25 – 195CytoplasmicSequence analysisAdd BLAST171
Transmembranei196 – 216HelicalSequence analysisAdd BLAST21
Topological domaini217 – 314ExtracellularSequence analysisAdd BLAST98

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000153982
PharmGKBiPA134879258

Polymorphism and mutation databases

BioMutaiGDPD1
DMDMi115502208

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002519311 – 314Lysophospholipase D GDPD1Add BLAST314

Proteomic databases

EPDiQ8N9F7
MaxQBiQ8N9F7
PaxDbiQ8N9F7
PeptideAtlasiQ8N9F7
PRIDEiQ8N9F7
ProteomicsDBi72526
72527 [Q8N9F7-2]
72528 [Q8N9F7-3]
TopDownProteomicsiQ8N9F7-2 [Q8N9F7-2]

PTM databases

iPTMnetiQ8N9F7
PhosphoSitePlusiQ8N9F7

Expressioni

Tissue specificityi

Widely expressed with high expression level in testis.1 Publication

Gene expression databases

BgeeiENSG00000153982 Expressed in 162 organ(s), highest expression level in primary visual cortex
CleanExiHS_GDPD1
ExpressionAtlasiQ8N9F7 baseline and differential
GenevisibleiQ8N9F7 HS

Interactioni

Protein-protein interaction databases

BioGridi129776, 27 interactors
IntActiQ8N9F7, 1 interactor
STRINGi9606.ENSP00000284116

Structurei

3D structure databases

ProteinModelPortaliQ8N9F7
SMRiQ8N9F7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini40 – 309GP-PDEAdd BLAST270

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258 Eukaryota
COG0584 LUCA
GeneTreeiENSGT00510000046745
HOGENOMiHOG000008170
HOVERGENiHBG054611
InParanoidiQ8N9F7
KOiK22387
OMAiRVCVGSF
OrthoDBiEOG091G0G89
PhylomeDBiQ8N9F7
TreeFamiTF328545

Family and domain databases

Gene3Di3.20.20.190, 2 hits
InterProiView protein in InterPro
IPR030395 GP_PDE_dom
IPR017946 PLC-like_Pdiesterase_TIM-brl
PfamiView protein in Pfam
PF03009 GDPD, 1 hit
SUPFAMiSSF51695 SSF51695, 1 hit
PROSITEiView protein in PROSITE
PS51704 GP_PDE, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 3 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q8N9F7-1) [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
MSSTAAFYLL STLGGYLVTS FLLLKYPTLL HQRKKQRFLS KHISHRGGAG
60 70 80 90 100
ENLENTMAAF QHAVKIGTDM LELDCHITKD EQVVVSHDEN LKRATGVNVN
110 120 130 140 150
ISDLKYCELP PYLGKLDVSF QRACQCEGKD NRIPLLKEVF EAFPNTPINI
160 170 180 190 200
DIKVNNNVLI KKVSELVKRY NREHLTVWGN ANYEIVEKCY KENSDIPILF
210 220 230 240 250
SLQRVLLILG LFFTGLLPFV PIREQFFEIP MPSIILKLKE PHTMSRSQKF
260 270 280 290 300
LIWLSDLLLM RKALFDHLTA RGIQVYIWVL NEEQEYKRAF DLGATGVMTD
310
YPTKLRDFLH NFSA
Length:314
Mass (Da):36,167
Last modified:October 3, 2006 - v2
Checksum:i8666D98E3A8084A9
GO
Isoform 2 (identifier: Q8N9F7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     276-290: YIWVLNEEQEYKRAF → SFWNDAFWKQHSSPV
     291-314: Missing.

Show »
Length:290
Mass (Da):33,363
Checksum:i554A9A22DC5DB5E2
GO
Isoform 3 (identifier: Q8N9F7-3) [UniParc]FASTAAdd to basket
Also known as: UGPQ

The sequence of this isoform differs from the canonical sequence as follows:
     266-314: DHLTARGIQVYIWVLNEEQEYKRAFDLGATGVMTDYPTKLRDFLHNFSA → EPLHPASKRNFEGHCSYLVVSCYF

Show »
Length:289
Mass (Da):33,220
Checksum:i17C52044B21A4A69
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
J3QQN7J3QQN7_HUMAN
Lysophospholipase D GDPD1
GDPD1
210Annotation score:
J3QRR6J3QRR6_HUMAN
Lysophospholipase D GDPD1
GDPD1
121Annotation score:
J3KTA9J3KTA9_HUMAN
Lysophospholipase D GDPD1
GDPD1
130Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti70M → T in BAC04419 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_020806266 – 314DHLTA…HNFSA → EPLHPASKRNFEGHCSYLVV SCYF in isoform 3. 1 PublicationAdd BLAST49
Alternative sequenceiVSP_020807276 – 290YIWVL…YKRAF → SFWNDAFWKQHSSPV in isoform 2. 1 PublicationAdd BLAST15
Alternative sequenceiVSP_020808291 – 314Missing in isoform 2. 1 PublicationAdd BLAST24

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY271346 mRNA Translation: AAQ01751.1
EU192951 mRNA Translation: ABW73991.1
AK094770 mRNA Translation: BAC04419.1
AC091059 Genomic DNA No translation available.
AC099850 Genomic DNA No translation available.
CH471109 Genomic DNA Translation: EAW94412.1
BC034432 mRNA Translation: AAH34432.1
CCDSiCCDS11616.1 [Q8N9F7-1]
CCDS58583.1 [Q8N9F7-3]
CCDS58584.1 [Q8N9F7-2]
RefSeqiNP_001159465.1, NM_001165993.1 [Q8N9F7-3]
NP_001159466.1, NM_001165994.1 [Q8N9F7-2]
NP_872375.2, NM_182569.3 [Q8N9F7-1]
UniGeneiHs.631744

Genome annotation databases

EnsembliENST00000284116; ENSP00000284116; ENSG00000153982 [Q8N9F7-1]
ENST00000581140; ENSP00000463273; ENSG00000153982 [Q8N9F7-3]
ENST00000581276; ENSP00000464690; ENSG00000153982 [Q8N9F7-2]
GeneIDi284161
KEGGihsa:284161
UCSCiuc002ixj.4 human [Q8N9F7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY271346 mRNA Translation: AAQ01751.1
EU192951 mRNA Translation: ABW73991.1
AK094770 mRNA Translation: BAC04419.1
AC091059 Genomic DNA No translation available.
AC099850 Genomic DNA No translation available.
CH471109 Genomic DNA Translation: EAW94412.1
BC034432 mRNA Translation: AAH34432.1
CCDSiCCDS11616.1 [Q8N9F7-1]
CCDS58583.1 [Q8N9F7-3]
CCDS58584.1 [Q8N9F7-2]
RefSeqiNP_001159465.1, NM_001165993.1 [Q8N9F7-3]
NP_001159466.1, NM_001165994.1 [Q8N9F7-2]
NP_872375.2, NM_182569.3 [Q8N9F7-1]
UniGeneiHs.631744

3D structure databases

ProteinModelPortaliQ8N9F7
SMRiQ8N9F7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi129776, 27 interactors
IntActiQ8N9F7, 1 interactor
STRINGi9606.ENSP00000284116

Chemistry databases

SwissLipidsiSLP:000001718

PTM databases

iPTMnetiQ8N9F7
PhosphoSitePlusiQ8N9F7

Polymorphism and mutation databases

BioMutaiGDPD1
DMDMi115502208

Proteomic databases

EPDiQ8N9F7
MaxQBiQ8N9F7
PaxDbiQ8N9F7
PeptideAtlasiQ8N9F7
PRIDEiQ8N9F7
ProteomicsDBi72526
72527 [Q8N9F7-2]
72528 [Q8N9F7-3]
TopDownProteomicsiQ8N9F7-2 [Q8N9F7-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000284116; ENSP00000284116; ENSG00000153982 [Q8N9F7-1]
ENST00000581140; ENSP00000463273; ENSG00000153982 [Q8N9F7-3]
ENST00000581276; ENSP00000464690; ENSG00000153982 [Q8N9F7-2]
GeneIDi284161
KEGGihsa:284161
UCSCiuc002ixj.4 human [Q8N9F7-1]

Organism-specific databases

CTDi284161
EuPathDBiHostDB:ENSG00000153982.10
GeneCardsiGDPD1
HGNCiHGNC:20883 GDPD1
MIMi616317 gene
neXtProtiNX_Q8N9F7
OpenTargetsiENSG00000153982
PharmGKBiPA134879258
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258 Eukaryota
COG0584 LUCA
GeneTreeiENSGT00510000046745
HOGENOMiHOG000008170
HOVERGENiHBG054611
InParanoidiQ8N9F7
KOiK22387
OMAiRVCVGSF
OrthoDBiEOG091G0G89
PhylomeDBiQ8N9F7
TreeFamiTF328545

Enzyme and pathway databases

BRENDAi3.1.4.46 2681
ReactomeiR-HSA-6814848 Glycerophospholipid catabolism

Miscellaneous databases

ChiTaRSiGDPD1 human
GenomeRNAii284161
PROiPR:Q8N9F7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000153982 Expressed in 162 organ(s), highest expression level in primary visual cortex
CleanExiHS_GDPD1
ExpressionAtlasiQ8N9F7 baseline and differential
GenevisibleiQ8N9F7 HS

Family and domain databases

Gene3Di3.20.20.190, 2 hits
InterProiView protein in InterPro
IPR030395 GP_PDE_dom
IPR017946 PLC-like_Pdiesterase_TIM-brl
PfamiView protein in Pfam
PF03009 GDPD, 1 hit
SUPFAMiSSF51695 SSF51695, 1 hit
PROSITEiView protein in PROSITE
PS51704 GP_PDE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiGDPD1_HUMAN
AccessioniPrimary (citable) accession number: Q8N9F7
Secondary accession number(s): A8W735, Q56VR1, Q8N4E3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 3, 2006
Last modified: September 12, 2018
This is version 119 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 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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