Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9HCC8 (GDPD2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:GDPD2
Synonyms:GDE3, OBDPF
ORF Names:UNQ1935/PRO4418
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length539 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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.

Catalytic activity

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

Cofactor

Calcium.

Subcellular location

Cell membrane; Multi-pass membrane protein. Cytoplasm. Cytoplasmcytoskeleton By similarity. Note: Colocalizes with the actin cytoskeleton By similarity.

Sequence similarities

Belongs to the glycerophosphoryl diester phosphodiesterase family.

Contains 1 GP-PDE domain.

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.

Sequence caution

The sequence BAA91014.1 differs from that shown. Reason: Frameshift at position 397.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9HCC8-1)

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.
Isoform 2 (identifier: Q9HCC8-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-79: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9HCC8-3)

The sequence of this isoform differs from the canonical sequence as follows:
     436-436: K → KDRFLLPAQAGLKLLASSNLPASASQSAGITGLSHCPPQPPGYKHELSHLAM
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 539539Glycerophosphoinositol inositolphosphodiesterase GDPD2
PRO_0000251934

Regions

Topological domain1 – 3838Cytoplasmic Potential
Transmembrane39 – 5921Helical; Potential
Topological domain60 – 8526Extracellular Potential
Transmembrane86 – 10621Helical; Potential
Topological domain107 – 12115Cytoplasmic Potential
Transmembrane122 – 14221Helical; Potential
Topological domain143 – 15412Extracellular Potential
Transmembrane155 – 17521Helical; Potential
Topological domain176 – 18813Cytoplasmic Potential
Transmembrane189 – 20921Helical; Potential
Topological domain210 – 490281Extracellular Potential
Transmembrane491 – 51121Helical; Potential
Topological domain512 – 53928Cytoplasmic Potential
Domain224 – 479256GP-PDE

Sites

Metal binding2561Divalent metal cation Potential
Metal binding2581Divalent metal cation Potential
Metal binding2711Divalent metal cation Potential

Amino acid modifications

Glycosylation4421N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence1 – 7979Missing in isoform 2.
VSP_042622
Alternative sequence4361K → KDRFLLPAQAGLKLLASSNL PASASQSAGITGLSHCPPQP PGYKHELSHLAM in isoform 3.
VSP_042623

Experimental info

Sequence conflict4181E → G in BAA91014. Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 8271C3A74766D540

FASTA53961,729
        10         20         30         40         50         60 
MAESPGCCSV WARCLHCLYS CHWRKCPRER MQTSKCDCIW FGLLFLTFLL SLSWLYIGLV 

        70         80         90        100        110        120 
LLNDLHNFNE FLFRRWGHWM DWSLAFLLVI SLLVTYASLL LVLALLLRLC RQPLHLHSLH 

       130        140        150        160        170        180 
KVLLLLIMLL VAAGLVGLDI QWQQEWHSLR VSLQATAPFL HIGAAAGIAL LAWPVADTFY 

       190        200        210        220        230        240 
RIHRRGPKIL LLLLFFGVVL VIYLAPLCIS SPCIMEPRDL PPKPGLVGHR GAPMLAPENT 

       250        260        270        280        290        300 
LMSLRKTAEC GATVFETDVM VSSDGVPFLM HDEHLSRTTN VASVFPTRIT AHSSDFSWTE 

       310        320        330        340        350        360 
LKRLNAGSWF LERRPFWGAK PLAGPDQKEA ESQTVPALEE LLEEAAALNL SIMFDLRRPP 

       370        380        390        400        410        420 
QNHTYYDTFV IQTLETVLNA RVPQAMVFWL PDEDRANVQR RAPGMRQIYG RQGGNRTERP 

       430        440        450        460        470        480 
QFLNLPYQDL PLLDIKALHK DNVSVNLFVV NKPWLFSLLW CAGVDSVTTN DCQLLQQMRY 

       490        500        510        520        530 
PIWLITPQTY LIIWVITNCV STMLLLWTFL LQRRFVKKRG KTGLETAVLL TRINNFMME 

« Hide

Isoform 2 [UniParc].

Checksum: 16081E6BAB94B16A
Show »

FASTA46052,186
Isoform 3 [UniParc].

Checksum: 1DC750F7411D9FDA
Show »

FASTA59066,991

References

« Hide 'large scale' references
[1]"Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation."
Yanaka N., Imai Y., Kawai E., Akatsuka H., Wakimoto K., Nogusa Y., Kato N., Chiba H., Kotani E., Omori K., Sakurai N.
J. Biol. Chem. 278:43595-43602(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Spleen.
[2]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[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. expand/collapse author list , 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] (ISOFORMS 1; 2 AND 3).
Tissue: Caudate nucleus, Colon mucosa and Spleen.
[4]"The DNA sequence of the human X chromosome."
Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. expand/collapse author list , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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 1).
Tissue: Skin.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001164662.1. NM_001171191.1.
NP_001164663.1. NM_001171192.1.
NP_001164664.1. NM_001171193.1.
NP_060181.2. NM_017711.3.
UniGeneHs.438712.

3D structure databases

ProteinModelPortalQ9HCC8.
SMRQ9HCC8. Positions 223-478.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid120207. 4 interactions.
IntActQ9HCC8. 41 interactions.
MINTMINT-1426959.
STRING9606.ENSP00000363503.

PTM databases

PhosphoSiteQ9HCC8.

Polymorphism databases

DMDM74752794.

Proteomic databases

PaxDbQ9HCC8.
PRIDEQ9HCC8.

Protocols and materials databases

DNASU54857.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000374382; ENSP00000363503; ENSG00000130055. [Q9HCC8-1]
ENST00000453994; ENSP00000414019; ENSG00000130055. [Q9HCC8-3]
ENST00000536730; ENSP00000445982; ENSG00000130055. [Q9HCC8-2]
ENST00000538649; ENSP00000444601; ENSG00000130055. [Q9HCC8-2]
GeneID54857.
KEGGhsa:54857.
UCSCuc004dyh.3. human. [Q9HCC8-1]
uc011mpk.2. human. [Q9HCC8-3]

Organism-specific databases

CTD54857.
GeneCardsGC0XP069642.
HGNCHGNC:25974. GDPD2.
HPAHPA045026.
neXtProtNX_Q9HCC8.
PharmGKBPA134907263.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0584.
HOGENOMHOG000232101.
HOVERGENHBG081551.
InParanoidQ9HCC8.
KOK01124.
OMAIKALHQD.
OrthoDBEOG7F511B.
PhylomeDBQ9HCC8.
TreeFamTF313692.

Enzyme and pathway databases

BRENDA3.1.4.46. 3474.

Gene expression databases

BgeeQ9HCC8.
CleanExHS_GDPD2.
GenevestigatorQ9HCC8.

Family and domain databases

Gene3D3.20.20.190. 1 hit.
InterProIPR004129. GlyceroP-diester-Pdiesterase.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PANTHERPTHR23344. PTHR23344. 1 hit.
PfamPF03009. GDPD. 1 hit.
[Graphical view]
SUPFAMSSF51695. SSF51695. 1 hit.
PROSITEPS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi54857.
NextBio57728.
PROQ9HCC8.

Entry information

Entry nameGDPD2_HUMAN
AccessionPrimary (citable) accession number: Q9HCC8
Secondary accession number(s): B4DRH4, B4DVC9, Q9NXJ6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: March 1, 2001
Last modified: April 16, 2014
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM