Q9NZC3 (GDE1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerophosphodiester phosphodiesterase 1
EC=3.1.4.44

Alternative name(s):
Membrane-interacting protein of RGS16
RGS16-interacting membrane protein

Gene names

Name:	GDE1
Synonyms:	MIR16

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	331 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Has glycerophosphoinositol phosphodiesterase activity. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways By similarity.
Catalytic activity	1-(sn-glycero-3-phospho)-1D-myo-inositol + H2O = myo-inositol + sn-glycerol 3-phosphate.
Cofactor	Magnesium By similarity.
Subunit structure	Interacts with RGS16 By similarity. Interacts with PRAF2. Ref.5
Subcellular location	Cytoplasm By similarity. Membrane; Multi-pass membrane protein By similarity. Note: Perinuclear vesicles and cell membrane By similarity.
Tissue specificity	Widely expressed. Ref.1
Post-translational modification	N-glycosylated By similarity.
Sequence similarities	Belongs to the glycerophosphoryl diester phosphodiesterase family. Contains 1 GDPD domain.
Sequence caution	The sequence AAC05440.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAC05803.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Cytoplasm Membrane
Coding sequence diversity	Polymorphism
Domain	Transmembrane Transmembrane helix
Ligand	Magnesium 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 Traceable author statement Ref.1. Source: UniProtKB
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Traceable author statement Ref.1. Source: UniProtKB
Molecular_function	glycerophosphodiester phosphodiesterase activity Traceable author statement Ref.1. Source: UniProtKB glycerophosphoinositol glycerophosphodiesterase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 331	331	Glycerophosphodiester phosphodiesterase 1		PRO_0000251944
Regions
	Topological domain	1 – 3	3	Cytoplasmic Potential
	Transmembrane	4 – 24	21	Helical; Potential
	Topological domain	25 – 247	223	Lumenal Potential
	Transmembrane	248 – 268	21	Helical; Potential
	Topological domain	269 – 331	63	Cytoplasmic Potential
	Domain	70 – 325	256	GDPD
Sites
	Metal binding	97	1	Magnesium Potential
	Metal binding	99	1	Magnesium Potential
	Metal binding	174	1	Magnesium Potential
Amino acid modifications
	Glycosylation	168	1	N-linked (GlcNAc...) Potential
	Glycosylation	198	1	N-linked (GlcNAc...) Potential
Natural variations
	Natural variant	218	1	R → Q. Corresponds to variant rs2072086 [ dbSNP | Ensembl ].		VAR_044018
	Natural variant	328	1	E → K. Corresponds to variant rs34137361 [ dbSNP | Ensembl ].		VAR_044019

Sequences

	Sequence		Length	Mass (Da)
	Q9NZC3 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: EFE567E71DBD4AC5	FASTA	331	37,718
	10 20 30 40 50 60 MWLWEDQGGL LGPFSFLLLV LLLVTRSPVN ACLLTGSLFV LLRVFSFEPV PSCRALQVLK 70 80 90 100 110 120 PRDRISAIAH RGGSHDAPEN TLAAIRQAAK NGATGVELDI EFTSDGIPVL MHDNTVDRTT 130 140 150 160 170 180 DGTGRLCDLT FEQIRKLNPA ANHRLRNDFP DEKIPTLREA VAECLNHNLT IFFDVKGHAH 190 200 210 220 230 240 KATEALKKMY MEFPQLYNNS VVCSFLPEVI YKMRQTDRDV ITALTHRPWS LSHTGDGKPR 250 260 270 280 290 300 YDTFWKHFIF VMMDILLDWS MHNILWYLCG ISAFLMQKDF VSPAYLKKWS AKGIQVVGWT 310 320 330 VNTFDEKSYY ESHLGSSYIT DSMVEDCEPH F

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"MIR16, a putative membrane glycerophosphodiester phosphodiesterase, interacts with RGS16." Zheng B., Chen D., Farquhar M.G. Proc. Natl. Acad. Sci. U.S.A. 97:3999-4004(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
[2]	"The role of GDE1/MIR16 in G protein-coupled receptor signaling." Duennebier F.F., Bachmann A.S. Submitted (NOV-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Brain.
[3]	"Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q." Loftus B.J., Kim U.-J., Sneddon V.P., Kalush F., Brandon R., Fuhrmann J., Mason T., Crosby M.L., Barnstead M., Cronin L., Mays A.D., Cao Y., Xu R.X., Kang H.-L., Mitchell S., Eichler E.E., Harris P.C., Venter J.C., Adams M.D. Genomics 60:295-308(1999) [PubMed] [Europe PMC] [Abstract] 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: B-cell, Brain, Colon and Kidney.
[5]	"Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase." Bachmann A.S., Duennebier F.F., Mocz G. Gene 371:144-153(2006) [PubMed] [Europe PMC] [Abstract] Cited for: 3D-STRUCTURE MODELING, INTERACTION WITH PRAF2.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF212862 mRNA. Translation: AAF65234.1. AY463154 mRNA. Translation: AAR25624.1. U91321 Genomic DNA. Translation: AAC05440.1. Sequence problems. AC003108 Genomic DNA. Translation: AAC05803.1. Sequence problems. BC014981 mRNA. Translation: AAH14981.1. BC025273 mRNA. Translation: AAH25273.1.
IPI	IPI00010279.
PIR	T01371.
RefSeq	NP_057725.1. NM_016641.3.
UniGene	Hs.512607.
3D structure databases
ProteinModelPortal	Q9NZC3.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9NZC3. 3 interactions.
STRING	9606.ENSP00000261386.
Polymorphism databases
DMDM	74734724.
Proteomic databases
PaxDb	Q9NZC3.
PRIDE	Q9NZC3.
Protocols and materials databases
DNASU	51573.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000353258; ENSP00000261386; ENSG00000006007.
GeneID	51573.
KEGG	hsa:51573.
UCSC	uc002dgh.3. human.
Organism-specific databases
CTD	51573.
GeneCards	GC16M019513.
HGNC	HGNC:29644. GDE1.
MIM	605943. gene.
neXtProt	NX_Q9NZC3.
PharmGKB	PA162389327.
GenAtlas	Search...
Phylogenomic databases
eggNOG	COG0584.
HOGENOM	HOG000006722.
HOVERGEN	HBG052946.
InParanoid	Q9NZC3.
OMA	AWTVNTF.
OrthoDB	EOG4D7Z61.
Enzyme and pathway databases
BRENDA	3.1.4.44. 2681.
Gene expression databases
ArrayExpress	Q9NZC3.
Bgee	Q9NZC3.
CleanEx	HS_GDE1.
Genevestigator	Q9NZC3.
GermOnline	ENSG00000006007. 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
ChiTaRS	GDE1. human.
GenomeRNAi	51573.
NextBio	55400.
SOURCE	Search...

Entry information

Entry name

GDE1_HUMAN

Accession

Primary (citable) accession number: Q9NZC3
Secondary accession number(s): O43334, Q6PKF7, Q7KYR4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 3, 2006
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 88 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.