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Q9NPB8 (GPCP1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | 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

Names and origin

Protein namesRecommended name:
Glycerophosphocholine phosphodiesterase GPCPD1

EC=3.1.4.2
Alternative name(s):
Glycerophosphodiester phosphodiesterase 5
Gene names
Name:GPCPD1
Synonyms:GDE5, KIAA1434
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length672 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity By similarity.

Catalytic activity

sn-glycero-3-phosphocholine + H2O = choline + sn-glycerol 3-phosphate.

Subcellular location

Cytoplasmcytosol By similarity.

Tissue specificity

Widely expressed, with highest expression in spinal chord.

Sequence similarities

Belongs to the glycerophosphoryl diester phosphodiesterase family.

Contains 1 CBM20 (carbohydrate binding type-20) domain.

Contains 1 GP-PDE domain.

Sequence caution

The sequence BAA91994.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAA92672.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 672672Glycerophosphocholine phosphodiesterase GPCPD1
PRO_0000050797

Regions

Domain1 – 115115CBM20
Domain318 – 618301GP-PDE
Region88 – 892Substrate binding Potential
Compositional bias169 – 1724Poly-Asp

Sites

Binding site701Substrate Potential

Amino acid modifications

Modified residue6081Phosphotyrosine By similarity

Natural variations

Natural variant2731T → I.
Corresponds to variant rs2273373 [ dbSNP | Ensembl ].
VAR_022060

Secondary structure

................... 672
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9NPB8 [UniParc].

Last modified October 10, 2002. Version 2.
Checksum: 9AA17024D231AD74

FASTA67276,035
        10         20         30         40         50         60 
MTPSQVAFEI RGTLLPGEVF AICGSCDALG NWNPQNAVAL LPENDTGESM LWKATIVLSR 

        70         80         90        100        110        120 
GVSVQYRYFK GYFLEPKTIG GPCQVIVHKW ETHLQPRSIT PLESEIIIDD GQFGIHNGVE 

       130        140        150        160        170        180 
TLDSGWLTCQ TEIRLRLHYS EKPPVSITKK KLKKSRFRVK LTLEGLEEDD DDRVSPTVLH 

       190        200        210        220        230        240 
KMSNSLEISL ISDNEFKCRH SQPECGYGLQ PDRWTEYSIQ TMEPDNLELI FDFFEEDLSE 

       250        260        270        280        290        300 
HVVQGDALPG HVGTACLLSS TIAESGKSAG ILTLPIMSRN SRKTIGKVRV DYIIIKPLPG 

       310        320        330        340        350        360 
YSCDMKSSFS KYWKPRIPLD VGHRGAGNST TTAQLAKVQE NTIASLRNAA SHGAAFVEFD 

       370        380        390        400        410        420 
VHLSKDFVPV VYHDLTCCLT MKKKFDADPV ELFEIPVKEL TFDQLQLLKL THVTALKSKD 

       430        440        450        460        470        480 
RKESVVQEEN SFSENQPFPS LKMVLESLPE DVGFNIEIKW ICQQRDGMWD GNLSTYFDMN 

       490        500        510        520        530        540 
LFLDIILKTV LENSGKRRIV FSSFDADICT MVRQKQNKYP ILFLTQGKSE IYPELMDLRS 

       550        560        570        580        590        600 
RTTPIAMSFA QFENLLGINV HTEDLLRNPS YIQEAKAKGL VIFCWGDDTN DPENRRKLKE 

       610        620        630        640        650        660 
LGVNGLIYDR IYDWMPEQPN IFQVEQLERL KQELPELKSC LCPTVSRFVP SSLCGESDIH 

       670 
VDANGIDNVE NA 

« Hide

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Kikuno R., Ishikawa K., Hirosawa M., Ohara O.
DNA Res. 7:65-73(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Brain.
[2]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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].
Tissue: Testis.
[5]"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] OF 413-672.
Tissue: Placenta.
[6]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)."
RIKEN structural genomics initiative (RSGI)
Submitted (MAY-2008) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-120 IN COMPLEX WITH PHOSPHATE.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB037855 mRNA. Translation: BAA92672.1. Different initiation.
AL109935 Genomic DNA. Translation: CAB91047.2.
CH471133 Genomic DNA. Translation: EAX10414.1.
CH471133 Genomic DNA. Translation: EAX10415.1.
BC027588 mRNA. Translation: AAH27588.1.
AK001947 mRNA. Translation: BAA91994.1. Different initiation.
CCDSCCDS13090.1.
RefSeqNP_062539.1. NM_019593.3.
XP_005260815.1. XM_005260758.2.
XP_006723658.1. XM_006723595.1.
XP_006723659.1. XM_006723596.1.
UniGeneHs.636359.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0BX-ray2.00A/B/C/D/E/F3-120[»]
ProteinModelPortalQ9NPB8.
SMRQ9NPB8. Positions 3-115, 321-611.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid121125. 1 interaction.
IntActQ9NPB8. 1 interaction.
MINTMINT-4650772.
STRING9606.ENSP00000368305.

Chemistry

BindingDBQ9NPB8.

Protein family/group databases

CAZyCBM20. Carbohydrate-Binding Module Family 20.

PTM databases

PhosphoSiteQ9NPB8.

Polymorphism databases

DMDM23821811.

Proteomic databases

MaxQBQ9NPB8.
PaxDbQ9NPB8.
PRIDEQ9NPB8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000379019; ENSP00000368305; ENSG00000125772.
GeneID56261.
KEGGhsa:56261.
UCSCuc002wmd.4. human.

Organism-specific databases

CTD56261.
GeneCardsGC20M005525.
HGNCHGNC:26957. GPCPD1.
HPAHPA039556.
HPA042987.
MIM614124. gene.
neXtProtNX_Q9NPB8.
PharmGKBPA165392351.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0584.
HOGENOMHOG000231653.
HOVERGENHBG080384.
InParanoidQ9NPB8.
OMAHDLTCCI.
OrthoDBEOG7RNJZM.
PhylomeDBQ9NPB8.
TreeFamTF314722.

Enzyme and pathway databases

ReactomeREACT_111217. Metabolism.

Gene expression databases

ArrayExpressQ9NPB8.
BgeeQ9NPB8.
GenevestigatorQ9NPB8.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
3.20.20.190. 1 hit.
InterProIPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR004129. GlyceroP-diester-Pdiesterase.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PfamPF00686. CBM_20. 1 hit.
PF03009. GDPD. 1 hit.
[Graphical view]
SMARTSM01065. CBM_2. 1 hit.
[Graphical view]
SUPFAMSSF49452. SSF49452. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEPS51166. CBM20. 1 hit.
PS51704. GP_PDE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSGPCPD1. human.
EvolutionaryTraceQ9NPB8.
GenomeRNAi56261.
NextBio61917.
PROQ9NPB8.
SOURCESearch...

Entry information

Entry nameGPCP1_HUMAN
AccessionPrimary (citable) accession number: Q9NPB8
Secondary accession number(s): D3DW06, Q9BQL8, Q9NUX0
Entry history
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 10, 2002
Last modified: July 9, 2014
This is version 115 of the entry and version 2 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM