Q9NPB8 (GPCP1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerophosphocholine phosphodiesterase GPCPD1
EC=3.1.4.2

Alternative name(s):
Glycerophosphodiester phosphodiesterase 5

Gene names

Name:	GPCPD1
Synonyms:	GDE5, KIAA1434

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	672 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Cytoplasm › cytosol 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 GDPD 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.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Polymorphism
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure 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	cytosol Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	carbohydrate binding Inferred from electronic annotation. Source: InterPro glycerophosphocholine phosphodiesterase activity Inferred from electronic annotation. Source: EC glycerophosphodiester phosphodiesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 672

672

Glycerophosphocholine phosphodiesterase GPCPD1

PRO_0000050797

Regions

Domain

1 – 115

115

CBM20

Domain

328 – 620

293

GDPD

Region

88 – 89

2

Substrate binding Potential

Compositional bias

169 – 172

4

Poly-Asp

Sites

Binding site

70

1

Substrate Potential

Amino acid modifications

Modified residue

608

1

Phosphotyrosine By similarity

Natural variations

Natural variant

273

1

T → I.
Corresponds to variant rs2273373 [ dbSNP | Ensembl ].

VAR_022060

Secondary structure

1

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672

Helix Strand Turn

Details...

Beta strand

4 – 11

8

Beta strand

19 – 26

8

Helix

27 – 29

3

Turn

30 – 32

3

Helix

34 – 36

3

Beta strand

49 – 58

10

Beta strand

64 – 74

11

Beta strand

84 – 90

7

Beta strand

97 – 99

3

Beta strand

103 – 112

10

Sequences

	Sequence		Length	Mass (Da)
	Q9NPB8 [UniParc]. Last modified October 10, 2002. Version 2. Checksum: 9AA17024D231AD74	FASTA	672	76,035
	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

References

	« Hide 'large scale' referencesShow '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: 10718198] [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: 11780052] [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. , 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: 15489334] [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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 413-672. Tissue: Placenta.
[6]	"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.

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.

IPI

IPI00099820.

RefSeq

NP_062539.1. NM_019593.3.

UniGene

Hs.636359.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2Z0B	X-ray	2.00	A/B/C/D/E/F	3-120	[»]

ProteinModelPortal

Q9NPB8.

SMR

Q9NPB8. Positions 3-115, 316-618.

ModBase

Search...

Protein family/group databases

CAZy

CBM20. Carbohydrate-Binding Module Family 20.

PTM databases

PhosphoSite

Q9NPB8.

Polymorphism databases

DMDM

23821811.

Proteomic databases

PRIDE

Q9NPB8.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000379019; ENSP00000368305; ENSG00000125772.

GeneID

56261.

KEGG

hsa:56261.

UCSC

uc002wmd.2. human.

Organism-specific databases

CTD

56261.

GeneCards

GC20M005525.

HGNC

HGNC:26957. GPCPD1.

HPA

HPA039556.

MIM

614124. gene.

neXtProt

NX_Q9NPB8.

PharmGKB

PA165392351.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

GeneTree

ENSGT00440000033970.

HOGENOM

HBG445186.

HOVERGEN

HBG080384.

InParanoid

Q9NPB8.

OMA

KQNKYPV.

OrthoDB

EOG47H5PP.

PhylomeDB

Q9NPB8.

Gene expression databases

ArrayExpress

Q9NPB8.

Bgee

Q9NPB8.

Genevestigator

Q9NPB8.

GermOnline

ENSG00000125772. Homo sapiens.

Family and domain databases

InterPro

IPR013784. Carb-bd-like_fold.
IPR002044. CBM_fam20.
IPR004129. GlyceroP-diester-Pdiesterase.
IPR013783. Ig-like_fold.
IPR017946. PLC-like_Pdiesterase_TIM-brl.
[Graphical view]

Gene3D

G3DSA:2.60.40.10. Ig-like_fold. 1 hit.
G3DSA:3.20.20.190. PLC-like_Pdiesterase_TIM-brl. 1 hit.

Pfam

PF00686. CBM_20. 1 hit.
PF03009. GDPD. 1 hit.
[Graphical view]

SMART

SM01065. CBM_2. 1 hit.
[Graphical view]

SUPFAM

SSF49452. CBD_4. 1 hit.
SSF51695. PLC-like_Pdiesterase_TIM-brl. 1 hit.

PROSITE

PS51166. CBM20. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

61917.

SOURCE

Search...

Entry information

Entry name

GPCP1_HUMAN

Accession

Primary (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:	January 25, 2012
This is version 92 of the entry and version 2 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.