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Protein

Glycerophosphoinositol inositolphosphodiesterase GDPD2

Gene

GDPD2

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

Functioni

Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4-phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity).By similarity

Catalytic activityi

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

Cofactori

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi256Divalent metal cationSequence analysis1
Metal bindingi258Divalent metal cationSequence analysis1
Metal bindingi271Divalent metal cationSequence analysis1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding

Enzyme and pathway databases

BioCyciZFISH:HS05338-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphoinositol inositolphosphodiesterase GDPD2 (EC:3.1.4.43)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 3
Glycerophosphodiester phosphodiesterase domain-containing protein 2
Osteoblast differentiation promoting factor
Gene namesi
Name:GDPD2
Synonyms:GDE3, OBDPF
ORF Names:UNQ1935/PRO4418
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:25974. GDPD2.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 38CytoplasmicSequence analysisAdd BLAST38
Transmembranei39 – 59HelicalSequence analysisAdd BLAST21
Topological domaini60 – 85ExtracellularSequence analysisAdd BLAST26
Transmembranei86 – 106HelicalSequence analysisAdd BLAST21
Topological domaini107 – 121CytoplasmicSequence analysisAdd BLAST15
Transmembranei122 – 142HelicalSequence analysisAdd BLAST21
Topological domaini143 – 154ExtracellularSequence analysisAdd BLAST12
Transmembranei155 – 175HelicalSequence analysisAdd BLAST21
Topological domaini176 – 188CytoplasmicSequence analysisAdd BLAST13
Transmembranei189 – 209HelicalSequence analysisAdd BLAST21
Topological domaini210 – 490ExtracellularSequence analysisAdd BLAST281
Transmembranei491 – 511HelicalSequence analysisAdd BLAST21
Topological domaini512 – 539CytoplasmicSequence analysisAdd BLAST28

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cytoplasm, Cytoskeleton, Membrane

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000130055.
PharmGKBiPA134907263.

Polymorphism and mutation databases

BioMutaiGDPD2.
DMDMi74752794.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002519341 – 539Glycerophosphoinositol inositolphosphodiesterase GDPD2Add BLAST539

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi442N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

PeptideAtlasiQ9HCC8.
PRIDEiQ9HCC8.

PTM databases

iPTMnetiQ9HCC8.
PhosphoSitePlusiQ9HCC8.

Expressioni

Gene expression databases

BgeeiENSG00000130055.
CleanExiHS_GDPD2.
GenevisibleiQ9HCC8. HS.

Organism-specific databases

HPAiHPA045026.

Interactioni

Protein-protein interaction databases

BioGridi120207. 4 interactors.
IntActiQ9HCC8. 41 interactors.
MINTiMINT-1426959.

Structurei

3D structure databases

ProteinModelPortaliQ9HCC8.
SMRiQ9HCC8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini224 – 479GP-PDEAdd BLAST256

Sequence similaritiesi

Contains 1 GP-PDE domain.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00510000046457.
HOGENOMiHOG000232101.
HOVERGENiHBG081551.
InParanoidiQ9HCC8.
KOiK01124.
OMAiIKALHQD.
OrthoDBiEOG091G043H.
PhylomeDBiQ9HCC8.
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]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q9HCC8-1) [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
MAESPGCCSV WARCLHCLYS CHWRKCPRER MQTSKCDCIW FGLLFLTFLL
60 70 80 90 100
SLSWLYIGLV LLNDLHNFNE FLFRRWGHWM DWSLAFLLVI SLLVTYASLL
110 120 130 140 150
LVLALLLRLC RQPLHLHSLH KVLLLLIMLL VAAGLVGLDI QWQQEWHSLR
160 170 180 190 200
VSLQATAPFL HIGAAAGIAL LAWPVADTFY RIHRRGPKIL LLLLFFGVVL
210 220 230 240 250
VIYLAPLCIS SPCIMEPRDL PPKPGLVGHR GAPMLAPENT LMSLRKTAEC
260 270 280 290 300
GATVFETDVM VSSDGVPFLM HDEHLSRTTN VASVFPTRIT AHSSDFSWTE
310 320 330 340 350
LKRLNAGSWF LERRPFWGAK PLAGPDQKEA ESQTVPALEE LLEEAAALNL
360 370 380 390 400
SIMFDLRRPP QNHTYYDTFV IQTLETVLNA RVPQAMVFWL PDEDRANVQR
410 420 430 440 450
RAPGMRQIYG RQGGNRTERP QFLNLPYQDL PLLDIKALHK DNVSVNLFVV
460 470 480 490 500
NKPWLFSLLW CAGVDSVTTN DCQLLQQMRY PIWLITPQTY LIIWVITNCV
510 520 530
STMLLLWTFL LQRRFVKKRG KTGLETAVLL TRINNFMME
Length:539
Mass (Da):61,729
Last modified:March 1, 2001 - v1
Checksum:i8271C3A74766D540
GO
Isoform 2 (identifier: Q9HCC8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-79: Missing.

Note: No experimental confirmation available.
Show »
Length:460
Mass (Da):52,186
Checksum:i16081E6BAB94B16A
GO
Isoform 3 (identifier: Q9HCC8-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     436-436: K → KDRFLLPAQAGLKLLASSNLPASASQSAGITGLSHCPPQPPGYKHELSHLAM

Note: No experimental confirmation available.
Show »
Length:590
Mass (Da):66,991
Checksum:i1DC750F7411D9FDA
GO

Sequence cautioni

The sequence BAA91014 differs from that shown. Reason: Frameshift at position 397.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti418E → G in BAA91014 (PubMed:14702039).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0426221 – 79Missing in isoform 2. 1 PublicationAdd BLAST79
Alternative sequenceiVSP_042623436K → KDRFLLPAQAGLKLLASSNL PASASQSAGITGLSHCPPQP PGYKHELSHLAM in isoform 3. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB048363 mRNA. Translation: BAB13350.1.
AY358986 mRNA. Translation: AAQ89345.1.
AK000214 mRNA. Translation: BAA91014.1. Frameshift.
AK299255 mRNA. Translation: BAG61286.1.
AK301025 mRNA. Translation: BAG62641.1.
AK316035 mRNA. Translation: BAH14406.1.
AL139398 Genomic DNA. Translation: CAI41020.1.
BC032009 mRNA. Translation: AAH32009.1.
CCDSiCCDS14402.1. [Q9HCC8-1]
CCDS55437.1. [Q9HCC8-3]
CCDS55438.1. [Q9HCC8-2]
RefSeqiNP_001164662.1. NM_001171191.1. [Q9HCC8-2]
NP_001164663.1. NM_001171192.1. [Q9HCC8-3]
NP_001164664.1. NM_001171193.1. [Q9HCC8-2]
NP_060181.2. NM_017711.3. [Q9HCC8-1]
UniGeneiHs.438712.

Genome annotation databases

EnsembliENST00000374382; ENSP00000363503; ENSG00000130055. [Q9HCC8-1]
ENST00000453994; ENSP00000414019; ENSG00000130055. [Q9HCC8-3]
ENST00000536730; ENSP00000445982; ENSG00000130055. [Q9HCC8-2]
ENST00000538649; ENSP00000444601; ENSG00000130055. [Q9HCC8-2]
GeneIDi54857.
KEGGihsa:54857.
UCSCiuc004dyh.4. human. [Q9HCC8-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB048363 mRNA. Translation: BAB13350.1.
AY358986 mRNA. Translation: AAQ89345.1.
AK000214 mRNA. Translation: BAA91014.1. Frameshift.
AK299255 mRNA. Translation: BAG61286.1.
AK301025 mRNA. Translation: BAG62641.1.
AK316035 mRNA. Translation: BAH14406.1.
AL139398 Genomic DNA. Translation: CAI41020.1.
BC032009 mRNA. Translation: AAH32009.1.
CCDSiCCDS14402.1. [Q9HCC8-1]
CCDS55437.1. [Q9HCC8-3]
CCDS55438.1. [Q9HCC8-2]
RefSeqiNP_001164662.1. NM_001171191.1. [Q9HCC8-2]
NP_001164663.1. NM_001171192.1. [Q9HCC8-3]
NP_001164664.1. NM_001171193.1. [Q9HCC8-2]
NP_060181.2. NM_017711.3. [Q9HCC8-1]
UniGeneiHs.438712.

3D structure databases

ProteinModelPortaliQ9HCC8.
SMRiQ9HCC8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120207. 4 interactors.
IntActiQ9HCC8. 41 interactors.
MINTiMINT-1426959.

PTM databases

iPTMnetiQ9HCC8.
PhosphoSitePlusiQ9HCC8.

Polymorphism and mutation databases

BioMutaiGDPD2.
DMDMi74752794.

Proteomic databases

PeptideAtlasiQ9HCC8.
PRIDEiQ9HCC8.

Protocols and materials databases

DNASUi54857.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000374382; ENSP00000363503; ENSG00000130055. [Q9HCC8-1]
ENST00000453994; ENSP00000414019; ENSG00000130055. [Q9HCC8-3]
ENST00000536730; ENSP00000445982; ENSG00000130055. [Q9HCC8-2]
ENST00000538649; ENSP00000444601; ENSG00000130055. [Q9HCC8-2]
GeneIDi54857.
KEGGihsa:54857.
UCSCiuc004dyh.4. human. [Q9HCC8-1]

Organism-specific databases

CTDi54857.
GeneCardsiGDPD2.
HGNCiHGNC:25974. GDPD2.
HPAiHPA045026.
MIMi300940. gene.
neXtProtiNX_Q9HCC8.
OpenTargetsiENSG00000130055.
PharmGKBiPA134907263.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00510000046457.
HOGENOMiHOG000232101.
HOVERGENiHBG081551.
InParanoidiQ9HCC8.
KOiK01124.
OMAiIKALHQD.
OrthoDBiEOG091G043H.
PhylomeDBiQ9HCC8.
TreeFamiTF313692.

Enzyme and pathway databases

BioCyciZFISH:HS05338-MONOMER.

Miscellaneous databases

GenomeRNAii54857.
PROiQ9HCC8.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000130055.
CleanExiHS_GDPD2.
GenevisibleiQ9HCC8. 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 nameiGDPD2_HUMAN
AccessioniPrimary (citable) accession number: Q9HCC8
Secondary accession number(s): B4DRH4, B4DVC9, Q9NXJ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: March 1, 2001
Last modified: November 2, 2016
This is version 128 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

Caution

The catalytic domain of GDPD2 is oriented extracellularly; Glycerophosphoinositol is hydrolyzed in the medium of cells overexpressing Gdpd2, whereas intracellular levels of glycerophosphoinositol is not affected.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: 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.