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Q9NPB8

- GPCP1_HUMAN

UniProt

Q9NPB8 - GPCP1_HUMAN

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Protein

Glycerophosphocholine phosphodiesterase GPCPD1

Gene

GPCPD1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei70 – 701SubstrateSequence Analysis

GO - Molecular functioni

  1. glycerophosphocholine phosphodiesterase activity Source: UniProtKB-EC
  2. starch binding Source: InterPro

GO - Biological processi

  1. glycerophospholipid biosynthetic process Source: Reactome
  2. phospholipid metabolic process Source: Reactome
  3. small molecule metabolic process Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Enzyme and pathway databases

ReactomeiREACT_120785. Hydrolysis of LPE.
REACT_120977. Hydrolysis of LPC.

Protein family/group databases

CAZyiCBM20. Carbohydrate-Binding Module Family 20.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycerophosphocholine phosphodiesterase GPCPD1 (EC:3.1.4.2)
Alternative name(s):
Glycerophosphodiester phosphodiesterase 5
Gene namesi
Name:GPCPD1
Synonyms:GDE5, KIAA1434
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 20

Organism-specific databases

HGNCiHGNC:26957. GPCPD1.

Subcellular locationi

Cytoplasmcytosol By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA165392351.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 672672Glycerophosphocholine phosphodiesterase GPCPD1PRO_0000050797Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei608 – 6081PhosphotyrosineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9NPB8.
PaxDbiQ9NPB8.
PRIDEiQ9NPB8.

PTM databases

PhosphoSiteiQ9NPB8.

Expressioni

Tissue specificityi

Widely expressed, with highest expression in spinal chord.

Gene expression databases

BgeeiQ9NPB8.
ExpressionAtlasiQ9NPB8. baseline and differential.
GenevestigatoriQ9NPB8.

Organism-specific databases

HPAiHPA039556.
HPA042987.

Interactioni

Protein-protein interaction databases

BioGridi121125. 1 interaction.
IntActiQ9NPB8. 1 interaction.
MINTiMINT-4650772.
STRINGi9606.ENSP00000368305.

Structurei

Secondary structure

1
672
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Beta strandi19 – 268Combined sources
Helixi27 – 293Combined sources
Turni30 – 323Combined sources
Helixi34 – 363Combined sources
Beta strandi49 – 5810Combined sources
Beta strandi64 – 7411Combined sources
Beta strandi84 – 907Combined sources
Beta strandi97 – 993Combined sources
Beta strandi103 – 11210Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z0BX-ray2.00A/B/C/D/E/F3-120[»]
ProteinModelPortaliQ9NPB8.
SMRiQ9NPB8. Positions 3-115, 321-611.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NPB8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 115115CBM20PROSITE-ProRule annotationAdd
BLAST
Domaini318 – 618301GP-PDEAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni88 – 892Substrate bindingSequence Analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi169 – 1724Poly-Asp

Sequence similaritiesi

Contains 1 CBM20 (carbohydrate binding type-20) domain.PROSITE-ProRule annotation
Contains 1 GP-PDE domain.Curated

Phylogenomic databases

eggNOGiCOG0584.
GeneTreeiENSGT00440000033970.
HOGENOMiHOG000231653.
HOVERGENiHBG080384.
InParanoidiQ9NPB8.
OMAiHDLTCCI.
OrthoDBiEOG7RNJZM.
PhylomeDBiQ9NPB8.
TreeFamiTF314722.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.20.20.190. 1 hit.
InterProiIPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]
PfamiPF00686. CBM_20. 1 hit.
[Graphical view]
SMARTiSM01065. CBM_2. 1 hit.
[Graphical view]
SUPFAMiSSF49452. SSF49452. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEiPS51166. CBM20. 1 hit.
PS51704. GP_PDE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9NPB8-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTPSQVAFEI RGTLLPGEVF AICGSCDALG NWNPQNAVAL LPENDTGESM
60 70 80 90 100
LWKATIVLSR GVSVQYRYFK GYFLEPKTIG GPCQVIVHKW ETHLQPRSIT
110 120 130 140 150
PLESEIIIDD GQFGIHNGVE TLDSGWLTCQ TEIRLRLHYS EKPPVSITKK
160 170 180 190 200
KLKKSRFRVK LTLEGLEEDD DDRVSPTVLH KMSNSLEISL ISDNEFKCRH
210 220 230 240 250
SQPECGYGLQ PDRWTEYSIQ TMEPDNLELI FDFFEEDLSE HVVQGDALPG
260 270 280 290 300
HVGTACLLSS TIAESGKSAG ILTLPIMSRN SRKTIGKVRV DYIIIKPLPG
310 320 330 340 350
YSCDMKSSFS KYWKPRIPLD VGHRGAGNST TTAQLAKVQE NTIASLRNAA
360 370 380 390 400
SHGAAFVEFD VHLSKDFVPV VYHDLTCCLT MKKKFDADPV ELFEIPVKEL
410 420 430 440 450
TFDQLQLLKL THVTALKSKD RKESVVQEEN SFSENQPFPS LKMVLESLPE
460 470 480 490 500
DVGFNIEIKW ICQQRDGMWD GNLSTYFDMN LFLDIILKTV LENSGKRRIV
510 520 530 540 550
FSSFDADICT MVRQKQNKYP ILFLTQGKSE IYPELMDLRS RTTPIAMSFA
560 570 580 590 600
QFENLLGINV HTEDLLRNPS YIQEAKAKGL VIFCWGDDTN DPENRRKLKE
610 620 630 640 650
LGVNGLIYDR IYDWMPEQPN IFQVEQLERL KQELPELKSC LCPTVSRFVP
660 670
SSLCGESDIH VDANGIDNVE NA
Length:672
Mass (Da):76,035
Last modified:October 10, 2002 - v2
Checksum:i9AA17024D231AD74
GO

Sequence cautioni

The sequence BAA91994.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAA92672.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti273 – 2731T → I.
Corresponds to variant rs2273373 [ dbSNP | Ensembl ].
VAR_022060

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS13090.1.
RefSeqiNP_062539.1. NM_019593.3.
XP_005260815.1. XM_005260758.2.
XP_006723658.1. XM_006723595.1.
XP_006723659.1. XM_006723596.1.
UniGeneiHs.636359.

Genome annotation databases

EnsembliENST00000379019; ENSP00000368305; ENSG00000125772.
GeneIDi56261.
KEGGihsa:56261.
UCSCiuc002wmd.4. human.

Polymorphism databases

DMDMi23821811.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSi CCDS13090.1.
RefSeqi NP_062539.1. NM_019593.3.
XP_005260815.1. XM_005260758.2.
XP_006723658.1. XM_006723595.1.
XP_006723659.1. XM_006723596.1.
UniGenei Hs.636359.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2Z0B X-ray 2.00 A/B/C/D/E/F 3-120 [» ]
ProteinModelPortali Q9NPB8.
SMRi Q9NPB8. Positions 3-115, 321-611.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 121125. 1 interaction.
IntActi Q9NPB8. 1 interaction.
MINTi MINT-4650772.
STRINGi 9606.ENSP00000368305.

Protein family/group databases

CAZyi CBM20. Carbohydrate-Binding Module Family 20.

PTM databases

PhosphoSitei Q9NPB8.

Polymorphism databases

DMDMi 23821811.

Proteomic databases

MaxQBi Q9NPB8.
PaxDbi Q9NPB8.
PRIDEi Q9NPB8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000379019 ; ENSP00000368305 ; ENSG00000125772 .
GeneIDi 56261.
KEGGi hsa:56261.
UCSCi uc002wmd.4. human.

Organism-specific databases

CTDi 56261.
GeneCardsi GC20M005525.
HGNCi HGNC:26957. GPCPD1.
HPAi HPA039556.
HPA042987.
MIMi 614124. gene.
neXtProti NX_Q9NPB8.
PharmGKBi PA165392351.
HUGEi Search...
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG0584.
GeneTreei ENSGT00440000033970.
HOGENOMi HOG000231653.
HOVERGENi HBG080384.
InParanoidi Q9NPB8.
OMAi HDLTCCI.
OrthoDBi EOG7RNJZM.
PhylomeDBi Q9NPB8.
TreeFami TF314722.

Enzyme and pathway databases

Reactomei REACT_120785. Hydrolysis of LPE.
REACT_120977. Hydrolysis of LPC.

Miscellaneous databases

ChiTaRSi GPCPD1. human.
EvolutionaryTracei Q9NPB8.
GenomeRNAii 56261.
NextBioi 61917.
PROi Q9NPB8.
SOURCEi Search...

Gene expression databases

Bgeei Q9NPB8.
ExpressionAtlasi Q9NPB8. baseline and differential.
Genevestigatori Q9NPB8.

Family and domain databases

Gene3Di 2.60.40.10. 1 hit.
3.20.20.190. 1 hit.
InterProi IPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view ]
Pfami PF00686. CBM_20. 1 hit.
[Graphical view ]
SMARTi SM01065. CBM_2. 1 hit.
[Graphical view ]
SUPFAMi SSF49452. SSF49452. 1 hit.
SSF51695. SSF51695. 1 hit.
PROSITEi PS51166. CBM20. 1 hit.
PS51704. GP_PDE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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.
    , 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. 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.

Entry informationi

Entry nameiGPCP1_HUMAN
AccessioniPrimary (citable) accession number: Q9NPB8
Secondary accession number(s): D3DW06, Q9BQL8, Q9NUX0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 10, 2002
Last sequence update: October 10, 2002
Last modified: November 26, 2014
This is version 119 of the entry and version 2 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3