Q9HCC8 (GDPD2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	GDPD2
Synonyms:	GDE3, OBDPF
ORF Names:	UNQ1935/PRO4418

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	539 AA.
Sequence status	Complete.
Protein existence	Evidence 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. Cytoplasm › cytoskeleton By similarity. Note: Colocalizes with the actin cytoskeleton By similarity.
Sequence similarities	Belongs to the glycerophosphoryl diester phosphodiesterase family. Contains 1 GDPD 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.

Ontologies

Keywords
Cellular component	Cell membrane Cytoplasm Cytoskeleton Membrane
Coding sequence diversity	Alternative splicing
Domain	Transmembrane Transmembrane helix
Ligand	Metal-binding
Molecular function	Hydrolase
PTM	Glycoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glycerol metabolic process Inferred from electronic annotation. Source: InterPro lipid metabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from direct assay. Source: HPA cytoskeleton Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	glycerophosphodiester phosphodiesterase activity Inferred from electronic annotation. Source: InterPro glycerophosphoinositol inositolphosphodiesterase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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 key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 539	539	Glycerophosphoinositol inositolphosphodiesterase GDPD2		PRO_0000251934
Regions
	Topological domain	1 – 38	38	Cytoplasmic Potential
	Transmembrane	39 – 59	21	Helical; Potential
	Topological domain	60 – 85	26	Extracellular Potential
	Transmembrane	86 – 106	21	Helical; Potential
	Topological domain	107 – 121	15	Cytoplasmic Potential
	Transmembrane	122 – 142	21	Helical; Potential
	Topological domain	143 – 154	12	Extracellular Potential
	Transmembrane	155 – 175	21	Helical; Potential
	Topological domain	176 – 188	13	Cytoplasmic Potential
	Transmembrane	189 – 209	21	Helical; Potential
	Topological domain	210 – 490	281	Extracellular Potential
	Transmembrane	491 – 511	21	Helical; Potential
	Topological domain	512 – 539	28	Cytoplasmic Potential
	Domain	229 – 474	246	GDPD
Sites
	Metal binding	256	1	Divalent metal cation Potential
	Metal binding	258	1	Divalent metal cation Potential
	Metal binding	271	1	Divalent metal cation Potential
Amino acid modifications
	Glycosylation	442	1	N-linked (GlcNAc...) Potential
Natural variations
	Alternative sequence	1 – 79	79	Missing in isoform 2.		VSP_042622
	Alternative sequence	436	1	K → KDRFLLPAQAGLKLLASSNL PASASQSAGITGLSHCPPQP PGYKHELSHLAM in isoform 3.		VSP_042623
Experimental info
	Sequence conflict	418	1	E → G in BAA91014. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: 8271C3A74766D540	FASTA	539	61,729
	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
	Isoform 2 [UniParc]. Checksum: 16081E6BAB94B16A	FASTA	460	52,186
	10 20 30 40 50 60 MDWSLAFLLV ISLLVTYASL LLVLALLLRL CRQPLHLHSL HKVLLLLIML LVAAGLVGLD 70 80 90 100 110 120 IQWQQEWHSL RVSLQATAPF LHIGAAAGIA LLAWPVADTF YRIHRRGPKI LLLLLFFGVV 130 140 150 160 170 180 LVIYLAPLCI SSPCIMEPRD LPPKPGLVGH RGAPMLAPEN TLMSLRKTAE CGATVFETDV 190 200 210 220 230 240 MVSSDGVPFL MHDEHLSRTT NVASVFPTRI TAHSSDFSWT ELKRLNAGSW FLERRPFWGA 250 260 270 280 290 300 KPLAGPDQKE AESQTVPALE ELLEEAAALN LSIMFDLRRP PQNHTYYDTF VIQTLETVLN 310 320 330 340 350 360 ARVPQAMVFW LPDEDRANVQ RRAPGMRQIY GRQGGNRTER PQFLNLPYQD LPLLDIKALH 370 380 390 400 410 420 KDNVSVNLFV VNKPWLFSLL WCAGVDSVTT NDCQLLQQMR YPIWLITPQT YLIIWVITNC 430 440 450 460 VSTMLLLWTF LLQRRFVKKR GKTGLETAVL LTRINNFMME
	Isoform 3 [UniParc]. Checksum: 1DC750F7411D9FDA	FASTA	590	66,991
	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 PLLDIKDRFL LPAQAGLKLL ASSNLPASAS QSAGITGLSH CPPQPPGYKH 490 500 510 520 530 540 ELSHLAMALH KDNVSVNLFV VNKPWLFSLL WCAGVDSVTT NDCQLLQQMR YPIWLITPQT 550 560 570 580 590 YLIIWVITNC VSTMLLLWTF LLQRRFVKKR GKTGLETAVL LTRINNFMME

References

	« Hide 'large scale' referencesShow '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. , 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. , 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. , 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.
IPI	IPI00102275. IPI00911110. IPI00954842.
RefSeq	NP_001164662.1. NM_001171191.1. NP_001164663.1. NM_001171192.1. NP_001164664.1. NM_001171193.1. NP_060181.2. NM_017711.3.
UniGene	Hs.438712.
3D structure databases
ProteinModelPortal	Q9HCC8.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9HCC8. 41 interactions.
MINT	MINT-1426959.
STRING	9606.ENSP00000363503.
PTM databases
PhosphoSite	Q9HCC8.
Polymorphism databases
DMDM	74752794.
Proteomic databases
PaxDb	Q9HCC8.
PRIDE	Q9HCC8.
Protocols and materials databases
DNASU	54857.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000374382; ENSP00000363503; ENSG00000130055. ENST00000453994; ENSP00000414019; ENSG00000130055. ENST00000536730; ENSP00000445982; ENSG00000130055. ENST00000538649; ENSP00000444601; ENSG00000130055.
GeneID	54857.
KEGG	hsa:54857.
UCSC	uc004dyh.3. human.
Organism-specific databases
CTD	54857.
GeneCards	GC0XP069642.
HGNC	HGNC:25974. GDPD2.
HPA	HPA045026.
neXtProt	NX_Q9HCC8.
PharmGKB	PA134907263.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG0584.
HOGENOM	HOG000232101.
HOVERGEN	HBG081551.
InParanoid	Q9HCC8.
KO	K01124.
OMA	IKALHQD.
OrthoDB	EOG42V8G2.
PhylomeDB	Q9HCC8.
Enzyme and pathway databases
BRENDA	3.1.4.46. 3474.
Gene expression databases
Bgee	Q9HCC8.
CleanEx	HS_GDPD2.
Genevestigator	Q9HCC8.
GermOnline	ENSG00000130055. Homo sapiens.
Family and domain databases
Gene3D	3.20.20.190. 1 hit.
InterPro	IPR004129. GlyceroP-diester-Pdiesterase. IPR017946. PLC-like_Pdiesterase_TIM-brl. [Graphical view]
PANTHER	PTHR23344. PTHR23344. 1 hit.
Pfam	PF03009. GDPD. 1 hit. [Graphical view]
SUPFAM	SSF51695. PLC-like_Pdiesterase_TIM-brl. 1 hit.
ProtoNet	Search...
Other
GenomeRNAi	54857.
NextBio	57728.

Entry information

Entry name

GDPD2_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 98 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.