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Protein

Glycerophosphodiester phosphodiesterase domain-containing protein 1

Gene

GDPD1

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

Functioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi72 – 721Divalent metal cationSequence analysis
Metal bindingi74 – 741Divalent metal cationSequence analysis
Metal bindingi87 – 871Divalent metal cationSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BRENDAi3.1.4.46. 2681.
ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphodiester phosphodiesterase domain-containing protein 1 (EC:3.1.-.-)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 4
Gene namesi
Name:GDPD1
Synonyms:GDE4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:20883. GDPD1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 33ExtracellularSequence analysis
Transmembranei4 – 2421HelicalSequence analysisAdd
BLAST
Topological domaini25 – 195171CytoplasmicSequence analysisAdd
BLAST
Transmembranei196 – 21621HelicalSequence analysisAdd
BLAST
Topological domaini217 – 31498ExtracellularSequence analysisAdd
BLAST

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134879258.

Polymorphism and mutation databases

BioMutaiGDPD1.
DMDMi115502208.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 314314Glycerophosphodiester phosphodiesterase domain-containing protein 1PRO_0000251931Add
BLAST

Proteomic databases

EPDiQ8N9F7.
MaxQBiQ8N9F7.
PaxDbiQ8N9F7.
PRIDEiQ8N9F7.
TopDownProteomicsiQ8N9F7-2. [Q8N9F7-2]

PTM databases

iPTMnetiQ8N9F7.
PhosphoSiteiQ8N9F7.

Expressioni

Tissue specificityi

Detected in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes.1 Publication

Gene expression databases

BgeeiQ8N9F7.
CleanExiHS_GDPD1.
ExpressionAtlasiQ8N9F7. baseline and differential.
GenevisibleiQ8N9F7. HS.

Interactioni

Protein-protein interaction databases

BioGridi129776. 27 interactions.
IntActiQ8N9F7. 1 interaction.
STRINGi9606.ENSP00000284116.

Structurei

3D structure databases

ProteinModelPortaliQ8N9F7.
SMRiQ8N9F7. Positions 36-199.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini40 – 309270GP-PDEAdd
BLAST

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ8N9F7.
OMAiQYRREHI.
PhylomeDBiQ8N9F7.
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 (3)i

Sequence statusi: Complete.

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

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

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti70 – 701M → T in BAC04419 (PubMed:14702039).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei266 – 31449DHLTA…HNFSA → EPLHPASKRNFEGHCSYLVV SCYF in isoform 3. 1 PublicationVSP_020806Add
BLAST
Alternative sequencei276 – 29015YIWVL…YKRAF → SFWNDAFWKQHSSPV in isoform 2. 1 PublicationVSP_020807Add
BLAST
Alternative sequencei291 – 31424Missing in isoform 2. 1 PublicationVSP_020808Add
BLAST

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

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. Positions 36-199.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi129776. 27 interactions.
IntActiQ8N9F7. 1 interaction.
STRINGi9606.ENSP00000284116.

PTM databases

iPTMnetiQ8N9F7.
PhosphoSiteiQ8N9F7.

Polymorphism and mutation databases

BioMutaiGDPD1.
DMDMi115502208.

Proteomic databases

EPDiQ8N9F7.
MaxQBiQ8N9F7.
PaxDbiQ8N9F7.
PRIDEiQ8N9F7.
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.
GeneCardsiGDPD1.
HGNCiHGNC:20883. GDPD1.
MIMi616317. gene.
neXtProtiNX_Q8N9F7.
PharmGKBiPA134879258.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2258. Eukaryota.
COG0584. LUCA.
GeneTreeiENSGT00510000046745.
HOGENOMiHOG000008170.
HOVERGENiHBG054611.
InParanoidiQ8N9F7.
OMAiQYRREHI.
PhylomeDBiQ8N9F7.
TreeFamiTF328545.

Enzyme and pathway databases

BRENDAi3.1.4.46. 2681.
ReactomeiR-HSA-6814848. Glycerophospholipid catabolism.

Miscellaneous databases

ChiTaRSiGDPD1. human.
GenomeRNAii284161.
PROiQ8N9F7.
SOURCEiSearch...

Gene expression databases

BgeeiQ8N9F7.
CleanExiHS_GDPD1.
ExpressionAtlasiQ8N9F7. baseline and differential.
GenevisibleiQ8N9F7. 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...

Publicationsi

« Hide 'large scale' publications
  1. "A novel splice variant of human gene NPL, mainly expressed in human liver, kidney and peripheral blood leukocyte."
    Wu M., Gu S., Xu J., Zou X., Zheng H., Jin Z., Xie Y., Ji C., Mao Y.
    DNA Seq. 16:137-142(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), TISSUE SPECIFICITY.
    Tissue: Fetal brain.
  2. "Isolation, characterization and molecular 3D model of human GDE4, a novel membrane protein containing glycerophosphodiester phosphodiesterase domain."
    Chang P.A., Shao H.B., Long D.X., Sun Q., Wu Y.J.
    Mol. Membr. Biol. 25:557-566(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, 3D-STRUCTURE MODELING.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  4. "DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
    Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L.
    , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
    Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "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] (ISOFORM 2).
    Tissue: Brain.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiGDPD1_HUMAN
AccessioniPrimary (citable) accession number: Q8N9F7
Secondary accession number(s): A8W735, Q56VR1, Q8N4E3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: October 3, 2006
Last modified: June 8, 2016
This is version 101 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: 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.