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Q9ESM6 (GDPD2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 83. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·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
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length539 AA.
Sequence statusComplete.
Protein existenceEvidence at protein 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. Ref.1 Ref.5

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. Note: Colocalizes with the actin cytoskeleton. Ref.1

Tissue specificity

Detected in spleen, femur and calvaria. Ref.1 Ref.4

Developmental stage

Up-regulated during osteoblast differentiation. Detected at low levels in mature osteoblasts.

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.

Biophysicochemical properties

Kinetic parameters:

KM=97.2 mM for glycerophosphoinositol Ref.5

Vmax=1.9 nmol/min/mg enzyme

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 539539Glycerophosphoinositol inositolphosphodiesterase GDPD2
PRO_0000251935

Regions

Topological domain1 – 4040Cytoplasmic Potential
Transmembrane41 – 6121Helical; Potential
Topological domain62 – 8322Extracellular Potential
Transmembrane84 – 10421Helical; Potential
Topological domain105 – 12117Cytoplasmic Potential
Transmembrane122 – 14221Helical; Potential
Topological domain143 – 15412Extracellular Potential
Transmembrane155 – 17521Helical; Potential
Topological domain176 – 18914Cytoplasmic Potential
Transmembrane190 – 21021Helical; Potential
Topological domain211 – 491281Extracellular Potential
Transmembrane492 – 51221Helical; Potential
Topological domain513 – 53927Cytoplasmic Potential
Domain230 – 475246GDPD

Sites

Metal binding2571Divalent metal cation Potential
Metal binding2591Divalent metal cation Potential
Metal binding2721Divalent metal cation Potential

Amino acid modifications

Glycosylation3331N-linked (GlcNAc...) Potential

Experimental info

Mutagenesis2311R → A: Loss of activity. Ref.5

Sequences

Sequence LengthMass (Da)Tools
Q9ESM6 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: B8A63DF2D6532BA2

FASTA53961,165
        10         20         30         40         50         60 
MADSPGCCSI WARCLHCLYS CHWRKYPKQK MQTSKCDCIW FGLLFLTFLL SLGWLYIGLI 

        70         80         90        100        110        120 
LLNDLHNFNE FLFRHWGHWM DWSLIVLLVV SLLVTYASLL LLLGLLLQLC GQPLHLHSLH 

       130        140        150        160        170        180 
KVLLLLIVLL VAAGLVGLDI QWRQEWHSLR LSLQATAPFL HIGAVAGITL LAWPVADTFY 

       190        200        210        220        230        240 
RIHPRGPKVL LLLLFFGVTL VIYLMPLLFI SSPCIMKLRD LPPKPGLVGH RGAPMLAPEN 

       250        260        270        280        290        300 
TLMSLRKTAE CGAAVFETDV MVSSDGVPFL MHDERLSRTT NVASVFPERI SAHSSDFSWA 

       310        320        330        340        350        360 
ELQRLNAGTW FLERQPFWGA KKLSGSDRKE AENQTIPALE ELLKEAAALN LSIMFDLRRP 

       370        380        390        400        410        420 
PRNHTYYDTF VNQTLEAVLS ANVSQAMVLW LPDEDRANVQ QRAPRMRQIY GHQGGNWTER 

       430        440        450        460        470        480 
PQFLNLPYQD LPALDIKALH QDNISVNLFV VNKPWLFSLL WCAGVDSVTT NACQLLQQMQ 

       490        500        510        520        530 
NPLWLLPPQK YLMIWVITDC ASILLLLSIF LLRGGCAKRN RTGLETAVLL TKINNFASE

« Hide

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], FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
Tissue: Osteoblast.
[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. expand/collapse author list , 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: Cecum.
[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]"Isolation and characterization of two serpentine membrane proteins containing glycerophosphodiester phosphodiesterase, GDE2 and GDE6."
Nogusa Y., Fujioka Y., Komatsu R., Kato N., Yanaka N.
Gene 337:173-179(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[5]"The developmentally regulated osteoblast phosphodiesterase GDE3 is glycerophosphoinositol-specific and modulates cell growth."
Corda D., Kudo T., Zizza P., Iurisci C., Kawai E., Kato N., Yanaka N., Mariggio S.
J. Biol. Chem. 284:24848-24856(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-231.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AB048364 mRNA. Translation: BAB13351.1.
AK018634 mRNA. Translation: BAB31318.1.
BC038274 mRNA. Translation: AAH38274.1.
IPIIPI00113411.
RefSeqNP_076097.1. NM_023608.3.
UniGeneMm.283495.

3D structure databases

ProteinModelPortalQ9ESM6.
SMRQ9ESM6. Positions 225-471.
ModBaseSearch...

PTM databases

PhosphoSiteQ9ESM6.

Proteomic databases

PaxDbQ9ESM6.
PRIDEQ9ESM6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000019503; ENSMUSP00000019503; ENSMUSG00000019359.
ENSMUST00000113744; ENSMUSP00000109373; ENSMUSG00000019359.
GeneID71584.
KEGGmmu:71584.

Organism-specific databases

CTD54857.
MGIMGI:1918834. Gdpd2.

Phylogenomic databases

eggNOGCOG0584.
GeneTreeENSGT00510000046457.
HOGENOMHOG000232101.
HOVERGENHBG081551.
InParanoidQ9ESM6.
KOK01124.
OrthoDBEOG42V8G2.

Enzyme and pathway databases

BRENDA3.1.4.46. 2681.
SABIO-RKQ9ESM6.

Gene expression databases

ArrayExpressQ9ESM6.
BgeeQ9ESM6.
GenevestigatorQ9ESM6.
GermOnlineENSMUSG00000019359. Mus musculus.

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. PLC-like_Pdiesterase_TIM-brl. 1 hit.
ProtoNetSearch...

Other

NextBio334047.
SOURCESearch...

Entry information

Entry nameGDPD2_MOUSE
AccessionPrimary (citable) accession number: Q9ESM6
Entry history
Integrated into UniProtKB/Swiss-Prot: October 3, 2006
Last sequence update: March 1, 2001
Last modified: May 1, 2013
This is version 83 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

MGD cross-references

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

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents