Q02979 (GDE1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glycerophosphodiester phosphodiesterase GDE1
EC=3.1.4.46

Gene names

Name:	GDE1
Ordered Locus Names:	YPL110C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	1223 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Glycerophosphocholine glycerophosphodiesterase responsible for the hydrolysis of intracellular glycerophosphocholine into glycerol-phosphate and choline. The choline is used for phosphatidyl-choline synthesis. Required for utilization of glycerophosphocholine as phosphate source. Ref.5 Ref.6
Catalytic activity	A glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.
Subcellular location	Cytoplasm Ref.3.
Miscellaneous	Present with 2300 molecules/cell in log phase SD medium. Ref.4
Sequence similarities	Belongs to the GDE1 family. Contains 6 ANK repeats. Contains 1 GDPD domain. Contains 1 SPX domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Domain	ANK repeat Repeat
Molecular function	Hydrolase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	glycerol metabolic process Inferred from electronic annotation. Source: InterPro glycerophospholipid catabolic process Inferred from mutant phenotype Ref.5. Source: SGD intracellular signal transduction Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from direct assay Ref.3. Source: SGD
Molecular function	glycerophosphocholine phosphodiesterase activity Inferred from mutant phenotype Ref.5. Source: SGD glycerophosphodiester phosphodiesterase activity Inferred from electronic annotation. Source: EC phospholipase C 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 – 1223	1223	Glycerophosphodiester phosphodiesterase GDE1		PRO_0000233009
Regions
	Domain	1 – 213	213	SPX
	Repeat	427 – 456	30	ANK 1
	Repeat	472 – 502	31	ANK 2
	Repeat	504 – 533	30	ANK 3
	Repeat	538 – 567	30	ANK 4
	Repeat	572 – 601	30	ANK 5
	Repeat	605 – 634	30	ANK 6
	Domain	877 – 1212	336	GDPD
Amino acid modifications
	Modified residue	61	1	Phosphoserine Ref.8
	Modified residue	254	1	Phosphoserine Ref.8
	Modified residue	256	1	Phosphoserine Ref.8
	Modified residue	265	1	Phosphothreonine Ref.8
	Modified residue	653	1	Phosphoserine Ref.8
	Modified residue	965	1	Phosphoserine Ref.7

Sequences

	Sequence		Length	Mass (Da)
	Q02979 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: C42E74B3CB7FB382	FASTA	1,223	138,014
	10 20 30 40 50 60 MKFGKTFANH RIPEWSSQYV GYKSLKKMIK EITRLQEDIY RAHNKNSYDE GRPPTKMRDS 70 80 90 100 110 120 SNSAQNYLDS PKIQKLLASF FFAVDRDIEK VDTFYNSQYA EYKKRFERLL SSNQFNEIKS 130 140 150 160 170 180 TLVVDANKED AVAQTLLTKD TREMNMLLKG TSQASRLSYH KDDLIEIQSI LAELRKQFRN 190 200 210 220 230 240 LKWYAELNKR AFGKILKKLD KKVGTNQQMS TMKTRILPLQ FANDSLITKD LSLLKTIWEQ 250 260 270 280 290 300 VTFRINSYER VMRSTSPNAN ANDNTEFFKI ICVFIEEDDS KGLIRELTNL YSELSLIPTR 310 320 330 340 350 360 IMISVLNKAA LSKSLACIDA ILKVIPSLND SEDINRRNFF HHHIIAIGKL IRKQEILSRK 370 380 390 400 410 420 KKSQPSKYTN SEGEIVTDLR TLHTTLSAPA ESDSITEEEK SSACTLSYIL EELPIHLRPC 430 440 450 460 470 480 LFQHDNYKRT PLHYSCQYGL SEVTKLIIKL MKEWNIWNEI PIDDVSAFGD AESLTPLHLC 490 500 510 520 530 540 VLGAHPKTTE VLLQSLDPNV KLKSSSLLHL ATEWNNYPLL HVLLSSKRFD INYQDNELHE 550 560 570 580 590 600 TPLYLACRLN FFEAAVCLLY NGADLEIREK LFGWTAIFVA AAEGFTDIVK LLIANNANFD 610 620 630 640 650 660 IEDEGGWTPM EHAVLRGHLH IADMVQIRDE LVTHPHSQLN SGSEEKEPLN EISAGELNER 670 680 690 700 710 720 NENGNGGNKG SLGKLAGPIK SYGHRFLDNN ESLILITLGS NDTRNKSPSI SLSSEALAKV 730 740 750 760 770 780 IGLETDCALS LVISCNDSID KSSVILDLPL DDNVDAVDFK VPFKVDYSHT LYFDIVPTYG 790 800 810 820 830 840 TRSLETHNRI DCQKNNNNYV MARGVSMLNK SYSSVGVNRS ILNGSVTVPI IANHTLEILG 850 860 870 880 890 900 TLKFEYIIIT PFEHPQLPLE RTETYWKSLV STRVIGHRGL GKNNPNKSLQ IGENTVESFI 910 920 930 940 950 960 MAASLGASYV EFDVQLTKDN VPVVYHDFLV AETGVDIPMH ELTLEQFLDL NNADKEHIQR 970 980 990 1000 1010 1020 GAGHSPHHVN GADTALQKYR GRSVDDSDVS TLRRAWDLHD NDPNGKSNNA HWSDNRMRLT 1030 1040 1050 1060 1070 1080 KTFKKNNFKG NARGHSIASS FVTLKELFKK IPANVGFNIE CKFPMLDEAE EEELGQIMME 1090 1100 1110 1120 1130 1140 MNHWVDTVLK VVFDNANGRD IIFSSFHPDI CIMLSLKQPV IPILFLTEGG SEQMADLRAS 1150 1160 1170 1180 1190 1200 SLQNGIRFAK KWNLLGIVSA AAPILKAPRL VQVVKSNGLV CVTYGVDNND PENASIQIEA 1210 1220 GVDAVIVDSV LAIRRGLTKK NEK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed: 9169875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]	"Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae." Fisher E., Almaguer C., Holic R., Griac P., Patton-Vogt J. J. Biol. Chem. 280:36110-36117(2005) [PubMed: 16141200] [Abstract] Cited for: FUNCTION.
[6]	"Glycerophosphocholine catabolism as a new route for choline formation for phosphatidylcholine synthesis by the Kennedy pathway." Fernandez-Murray J.P., McMaster C.R. J. Biol. Chem. 280:38290-38296(2005) [PubMed: 16172116] [Abstract] Cited for: FUNCTION.
[7]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-965, MASS SPECTROMETRY.
[8]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-61; SER-254; SER-256; THR-265 AND SER-653, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U43503 Genomic DNA. Translation: AAB68251.1. BK006949 Genomic DNA. Translation: DAA11323.1.
PIR	S62011.
RefSeq	NP_015215.1. NM_001183924.1.
3D structure databases
ProteinModelPortal	Q02979.
SMR	Q02979. Positions 416-631, 871-1219.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-8774N.
IntAct	Q02979. 9 interactions.
MINT	MINT-394412.
STRING	Q02979.
Proteomic databases
PeptideAtlas	Q02979.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YPL110C; YPL110C; YPL110C.
GeneID	855994.
KEGG	sce:YPL110C.
NMPDR	fig|4932.3.peg.6347.
Organism-specific databases
CYGD	YPL110c.
SGD	S000006031. GDE1.
Phylogenomic databases
eggNOG	fuNOG04819.
GeneTree	EFGT00050000000625.
HOGENOM	HBG329172.
OMA	STRVIGH.
OrthoDB	EOG4WHCTV.
Gene expression databases
ArrayExpress	Q02979.
Genevestigator	Q02979.
GermOnline	YPL110C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR002110. Ankyrin_rpt. IPR020683. Ankyrin_rpt-contain_dom. IPR004129. GlyceroP-diester-Pdiesterase. IPR017946. PLC-like_Pdiesterase_TIM-brl. IPR000909. PLipase_C_PInositol-sp_X_dom. IPR004331. SPX_N. [Graphical view]
Gene3D	G3DSA:1.25.40.20. ANK. 1 hit. G3DSA:3.20.20.190. PLC-like_Pdiesterase_TIM-brl. 2 hits.
KO	K06867.
Pfam	PF12796. Ank_2. 1 hit. PF03009. GDPD. 1 hit. PF03105. SPX. 1 hit. [Graphical view]
SMART	SM00248. ANK. 7 hits. [Graphical view]
SUPFAM	SSF48403. ANK. 1 hit. SSF51695. PLC-like_Pdiesterase_TIM-brl. 1 hit.
PROSITE	PS50297. ANK_REP_REGION. 1 hit. PS50088. ANK_REPEAT. 2 hits. PS51382. SPX. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	980851.

Entry information

Entry name

GDE1_YEAST

Accession

Primary (citable) accession number: Q02979
Secondary accession number(s): D6W3Q7

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 18, 2006
Last sequence update:	November 1, 1996
Last modified:	December 14, 2011
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program