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Protein

Glycerophosphodiester phosphodiesterase 1

Gene

Gde1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi97 – 971MagnesiumSequence analysis
Metal bindingi99 – 991MagnesiumSequence analysis
Metal bindingi174 – 1741MagnesiumSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

ReactomeiR-MMU-6814848. Glycerophospholipid catabolism.

Chemistry

SwissLipidsiSLP:000001124.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase 1 (EC:3.1.4.44)
Alternative name(s):
Membrane-interacting protein of RGS16
Gene namesi
Name:Gde1
Synonyms:Mir16
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 7

Organism-specific databases

MGIiMGI:1891827. 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)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 33CytoplasmicSequence analysis
Transmembranei4 – 2421HelicalSequence analysisAdd
BLAST
Topological domaini25 – 248224LumenalSequence analysisAdd
BLAST
Transmembranei249 – 26921HelicalSequence analysisAdd
BLAST
Topological domaini270 – 33162CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

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

Keywords - Cellular componenti

Cell membrane, Cytoplasmic vesicle, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 331331Glycerophosphodiester phosphodiesterase 1PRO_0000251945Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi168 – 1681N-linked (GlcNAc...)Sequence analysis

Post-translational modificationi

N-glycosylated.By similarity

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9JL56.
MaxQBiQ9JL56.
PaxDbiQ9JL56.
PeptideAtlasiQ9JL56.
PRIDEiQ9JL56.

PTM databases

iPTMnetiQ9JL56.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiQ9JL56.
CleanExiMM_GDE1.
ExpressionAtlasiQ9JL56. baseline and differential.
GenevisibleiQ9JL56. MM.

Interactioni

Subunit structurei

Interacts with PRAF2 and RGS16.By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000046371.

Structurei

3D structure databases

ProteinModelPortaliQ9JL56.
SMRiQ9JL56. Positions 62-224.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini65 – 331267GP-PDEAdd
BLAST

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000047820.
HOGENOMiHOG000006722.
HOVERGENiHBG052946.
InParanoidiQ9JL56.
KOiK19179.
OMAiSPFNACL.
OrthoDBiEOG72JWGZ.
PhylomeDBiQ9JL56.
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.

Q9JL56-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MWLWEDQGGL LGPFSFVLVL LLVVTRSPFN ACVLTGSLYI LLRFFSFEPV
60 70 80 90 100
PSRRALQVLK PRDRVSAIAH RGGSHDAPEN TLAAIRQAAK NGATGVELDI
110 120 130 140 150
EFTSDGVPVL MHDNTVDRTT DGSGRLCDLT FEQVRKLNPA ANHRLRNEFP
160 170 180 190 200
DERIPTLKEA VTECLRHNLT IFFDVKGHAD MASAALKNIY TEFPQLYNNS
210 220 230 240 250
MVCSFLPEVI YKMRQTDQKV ITALTHRPWS LSHTGDGKPR YSVFWKQSVF
260 270 280 290 300
VVLDILLDWS MHNVLWYLCG ISAFLMQKDF VSPDYLKKWS AKGIQVVSWT
310 320 330
VNTFDEKNYY ESHLGSSYIT DSMLEDCAPH F
Length:331
Mass (Da):37,629
Last modified:October 1, 2000 - v1
Checksum:iC79A058AA884C10B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti102 – 1021F → L in BAE29870 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212860 mRNA. Translation: AAF65232.1.
AK005361 mRNA. Translation: BAB23975.1.
AK150807 mRNA. Translation: BAE29870.1.
BC003902 mRNA. Translation: AAH03902.1.
CCDSiCCDS21774.1.
RefSeqiNP_062526.1. NM_019580.4.
UniGeneiMm.273142.

Genome annotation databases

EnsembliENSMUST00000038791; ENSMUSP00000046371; ENSMUSG00000033917.
GeneIDi56209.
KEGGimmu:56209.
UCSCiuc009jki.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212860 mRNA. Translation: AAF65232.1.
AK005361 mRNA. Translation: BAB23975.1.
AK150807 mRNA. Translation: BAE29870.1.
BC003902 mRNA. Translation: AAH03902.1.
CCDSiCCDS21774.1.
RefSeqiNP_062526.1. NM_019580.4.
UniGeneiMm.273142.

3D structure databases

ProteinModelPortaliQ9JL56.
SMRiQ9JL56. Positions 62-224.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000046371.

Chemistry

SwissLipidsiSLP:000001124.

PTM databases

iPTMnetiQ9JL56.

Proteomic databases

EPDiQ9JL56.
MaxQBiQ9JL56.
PaxDbiQ9JL56.
PeptideAtlasiQ9JL56.
PRIDEiQ9JL56.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000038791; ENSMUSP00000046371; ENSMUSG00000033917.
GeneIDi56209.
KEGGimmu:56209.
UCSCiuc009jki.1. mouse.

Organism-specific databases

CTDi51573.
MGIiMGI:1891827. Gde1.

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000047820.
HOGENOMiHOG000006722.
HOVERGENiHBG052946.
InParanoidiQ9JL56.
KOiK19179.
OMAiSPFNACL.
OrthoDBiEOG72JWGZ.
PhylomeDBiQ9JL56.
TreeFamiTF313692.

Enzyme and pathway databases

ReactomeiR-MMU-6814848. Glycerophospholipid catabolism.

Miscellaneous databases

PROiQ9JL56.
SOURCEiSearch...

Gene expression databases

BgeeiQ9JL56.
CleanExiMM_GDE1.
ExpressionAtlasiQ9JL56. baseline and differential.
GenevisibleiQ9JL56. MM.

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...

Publicationsi

« Hide 'large scale' publications
  1. "MIR16, a putative membrane glycerophosphodiester phosphodiesterase, interacts with RGS16."
    Zheng B., Chen D., Farquhar M.G.
    Proc. Natl. Acad. Sci. U.S.A. 97:3999-4004(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow and Cerebellum.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: FVB/N.
    Tissue: Mammary tumor.
  4. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Kidney and Lung.

Entry informationi

Entry nameiGDE1_MOUSE
AccessioniPrimary (citable) accession number: Q9JL56
Secondary accession number(s): Q3UBU4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 1, 2000
Last modified: July 6, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.