Glycerophosphodiester phosphodiesterase GDE1 (Q02979)

Identification

Name

Glycerophosphodiester phosphodiesterase GDE1

Synonyms

Not Available

Gene Name

GDE1

Enzyme Class

3.1.4.46

Biological Properties

General Function

Involved in protein binding

Specific 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

Cellular Location

Cytoplasm

SMPDB Pathways

Lysolipid incorporation into ER PC(16:0/16:0)	PW002784
Lysolipid incorporation into ER PC(16:1(11Z)/16:1(11Z))	PW002786
Lysolipid incorporation into ER PC(16:1(9Z)/16:1(9Z))	PW002785
Lysolipid incorporation into ER PC(18:0/18:0)	PW002787
Lysolipid incorporation into ER PC(18:1(9Z)/18:1(9Z))	PW002788

KEGG Pathways

Glycerophospholipid metabolism

ec00564

SMPDB Reactions

Glycerophosphocholine + water → hydron + Glycerol 3-phosphate + Choline

Glycerophosphocholine + water → Ethanol + Choline

KEGG Reactions

water + Glycerophosphocholine → Glycerol 3-phosphate + Choline + hydron

Metabolites

YMDB ID	Name	View
YMDB00073	Glycerol 3-phosphate	Show
YMDB00227	Choline	Show
YMDB00309	Glycerophosphocholine	Show
YMDB00694	sn-Glycero-3-phosphocholine	Show
YMDB00862	hydron	Show
YMDB00883	Ethanol	Show
YMDB00890	water	Show
YMDB00988	sn-glycerol 3-phosphate	Show

GO Classification

Component
Not Available
Function
catalytic activity
lipase activity
phospholipase activity
phospholipase C activity
phosphoric diester hydrolase activity
glycerophosphodiester phosphodiesterase activity
hydrolase activity
hydrolase activity, acting on ester bonds
phosphoric ester hydrolase activity
Process
lipid metabolic process
metabolic process
primary metabolic process
small molecule metabolic process
alcohol metabolic process
polyol metabolic process
alditol metabolic process
glycerol metabolic process
signaling
signaling pathway
intracellular signaling pathway

Gene Properties

Chromosome Location

chromosome 16

Locus

YPL110C

Gene Sequence

>3672 bp ATGAAGTTCGGAAAAACCTTTGCCAATCATCGCATTCCAGAGTGGTCAAGTCAATATGTT GGCTACAAGTCGTTGAAGAAAATGATTAAAGAAATTACAAGACTTCAAGAAGACATATAT AGGGCACATAACAAGAATAGCTATGATGAAGGCAGGCCACCAACAAAAATGAGAGATTCA TCTAATAGTGCTCAAAATTATTTGGACTCTCCAAAAATCCAAAAGTTATTGGCGTCGTTT TTCTTTGCAGTTGACAGGGATATTGAGAAGGTTGATACATTTTACAATTCCCAGTATGCG GAATATAAGAAAAGATTTGAGAGATTGCTTTCTTCTAATCAATTCAATGAGATAAAATCA ACATTAGTGGTCGATGCCAACAAAGAAGATGCAGTAGCGCAAACCTTACTCACAAAGGAT ACGAGAGAGATGAATATGCTTTTAAAGGGAACAAGTCAAGCCAGCCGTCTATCTTACCAT AAAGATGACTTAATTGAAATTCAGTCTATCTTAGCTGAGTTAAGAAAACAATTTAGAAAC TTAAAGTGGTACGCTGAACTAAATAAGAGAGCTTTTGGTAAGATTTTAAAGAAACTGGAT AAAAAAGTCGGCACAAATCAGCAAATGTCAACTATGAAAACTAGAATCTTGCCGTTACAA TTTGCTAATGATTCTCTTATTACCAAAGATTTGAGTTTGCTAAAAACTATCTGGGAACAA GTGACGTTCAGGATAAATTCTTACGAGAGAGTAATGAGGAGTACCTCGCCGAACGCAAAT GCTAATGATAATACAGAATTCTTTAAGATTATTTGCGTTTTTATAGAAGAAGATGATAGC AAAGGATTGATTAGAGAGCTAACAAACCTATATTCGGAATTGTCTTTGATTCCAACAAGA ATTATGATAAGTGTTTTAAACAAGGCAGCACTGTCTAAATCACTGGCATGTATTGATGCT ATCTTAAAGGTTATTCCGTCTCTAAATGACTCGGAAGATATTAACAGAAGAAATTTTTTC CATCATCACATAATTGCAATCGGGAAGTTAATCAGAAAACAGGAAATTTTAAGTAGGAAA AAGAAGTCACAACCCTCAAAATATACTAATAGTGAGGGAGAAATTGTAACAGATTTAAGA ACCCTGCATACGACCCTATCTGCCCCGGCAGAATCAGATAGCATTACAGAGGAGGAAAAA AGTTCGGCCTGTACACTCTCTTATATTTTAGAGGAGTTACCAATTCATTTAAGACCATGC CTTTTTCAGCATGATAATTACAAGAGAACGCCCTTGCATTATTCTTGCCAGTATGGCTTA TCTGAAGTTACGAAGTTGATTATCAAGTTAATGAAAGAATGGAATATCTGGAATGAAATC CCTATTGATGACGTTTCCGCGTTCGGAGATGCCGAATCATTGACACCTTTACATTTATGT GTGTTGGGTGCTCATCCCAAAACAACAGAAGTCTTATTGCAATCTTTGGATCCGAACGTG AAATTAAAAAGTTCAAGTTTGTTACATTTGGCCACTGAGTGGAATAACTATCCCCTTTTA CATGTTCTCCTATCATCAAAAAGGTTTGATATTAATTATCAAGACAACGAATTACATGAA ACACCGCTATATCTTGCTTGTAGATTAAATTTTTTCGAAGCTGCTGTGTGTTTGTTGTAC AATGGAGCCGACCTTGAAATAAGAGAAAAACTTTTTGGCTGGACAGCTATCTTCGTTGCA GCAGCAGAAGGGTTTACGGACATTGTAAAGCTCTTGATAGCCAACAACGCGAACTTTGAT ATTGAAGATGAAGGTGGGTGGACGCCGATGGAGCACGCGGTATTGCGCGGTCATTTGCAC ATTGCTGATATGGTTCAAATCAGAGACGAACTGGTCACGCATCCCCATTCACAGTTGAAC AGTGGTAGCGAAGAGAAAGAACCACTAAACGAAATTAGTGCCGGAGAATTAAATGAGAGA AATGAAAATGGAAACGGAGGTAATAAAGGGTCCTTGGGAAAACTGGCCGGACCAATAAAG TCATATGGACACAGATTCCTGGATAATAATGAATCACTTATACTAATAACATTGGGAAGT AATGACACAAGAAACAAAAGCCCTTCAATTTCATTAAGCTCGGAAGCACTAGCAAAAGTT ATTGGGTTGGAAACAGATTGTGCATTATCGTTAGTAATTTCATGCAATGATTCAATTGAT AAATCTTCTGTAATCTTAGATTTACCATTAGATGATAATGTGGACGCAGTAGACTTCAAA GTGCCTTTCAAAGTTGATTATTCTCATACATTATATTTTGATATTGTGCCAACATATGGA ACACGCTCGTTGGAGACCCATAATAGAATAGATTGTCAAAAAAATAACAATAATTACGTA ATGGCAAGGGGTGTTTCCATGTTGAATAAGTCGTACAGCTCAGTGGGAGTTAATAGAAGT ATATTAAATGGTAGCGTGACGGTCCCCATCATCGCTAATCATACACTGGAGATACTTGGG ACGCTGAAATTTGAATATATTATTATCACACCATTTGAACATCCACAACTGCCCTTAGAA AGAACAGAAACGTACTGGAAATCCTTAGTGTCCACTCGTGTTATAGGACATAGAGGCCTG GGTAAAAATAATCCTAATAAATCATTACAAATTGGAGAGAACACAGTCGAGTCTTTCATC ATGGCAGCCTCATTGGGAGCATCGTATGTAGAGTTTGATGTTCAGTTGACGAAGGATAAC GTACCAGTGGTATATCACGATTTTCTCGTAGCTGAAACAGGTGTCGATATCCCCATGCAT GAATTGACGCTGGAACAGTTTTTAGATTTGAACAATGCCGATAAAGAGCACATTCAACGT GGAGCAGGTCACTCACCTCATCATGTAAATGGAGCAGATACAGCACTACAAAAATATAGA GGGCGTTCGGTAGATGATTCAGACGTTAGTACATTGAGGAGAGCTTGGGATTTACACGAC AACGACCCGAATGGGAAGTCCAACAATGCTCATTGGTCTGACAATCGAATGAGGCTAACC AAAACATTTAAAAAGAACAATTTTAAGGGAAACGCTAGAGGACATTCAATAGCTTCATCA TTTGTTACCTTGAAAGAACTATTCAAGAAAATCCCTGCCAACGTTGGGTTTAACATAGAA TGTAAGTTTCCCATGCTTGATGAGGCAGAAGAGGAAGAGTTAGGGCAAATAATGATGGAA ATGAACCATTGGGTTGACACCGTGTTAAAAGTAGTTTTTGACAATGCGAATGGTAGGGAC ATCATTTTTTCGTCATTTCATCCGGATATTTGCATCATGCTTTCGTTAAAGCAACCGGTT ATTCCGATCTTGTTCCTGACGGAAGGTGGAAGTGAACAGATGGCCGATTTGAGAGCCTCA TCGTTACAAAACGGTATAAGATTTGCTAAGAAGTGGAATTTATTGGGGATTGTATCTGCT GCAGCACCCATTTTAAAGGCCCCACGGTTGGTGCAAGTGGTTAAGTCTAATGGGCTGGTA TGTGTCACTTACGGTGTGGACAACAATGATCCCGAAAATGCCAGTATACAAATTGAAGCA GGTGTAGATGCCGTGATCGTCGATAGTGTATTGGCAATTAGACGTGGGTTAACCAAAAAG AATGAAAAGTAA

Protein Properties

Pfam Domain Function

GDPD (PF03009 )
SPX (PF03105 )

Protein Residues

1223

Protein Molecular Weight

138013.0

Protein Theoretical pI

6.77

Signalling Regions

None

Transmembrane Regions

None

Protein Sequence

>Glycerophosphodiester phosphodiesterase GDE1 MKFGKTFANHRIPEWSSQYVGYKSLKKMIKEITRLQEDIYRAHNKNSYDEGRPPTKMRDS SNSAQNYLDSPKIQKLLASFFFAVDRDIEKVDTFYNSQYAEYKKRFERLLSSNQFNEIKS TLVVDANKEDAVAQTLLTKDTREMNMLLKGTSQASRLSYHKDDLIEIQSILAELRKQFRN LKWYAELNKRAFGKILKKLDKKVGTNQQMSTMKTRILPLQFANDSLITKDLSLLKTIWEQ VTFRINSYERVMRSTSPNANANDNTEFFKIICVFIEEDDSKGLIRELTNLYSELSLIPTR IMISVLNKAALSKSLACIDAILKVIPSLNDSEDINRRNFFHHHIIAIGKLIRKQEILSRK KKSQPSKYTNSEGEIVTDLRTLHTTLSAPAESDSITEEEKSSACTLSYILEELPIHLRPC LFQHDNYKRTPLHYSCQYGLSEVTKLIIKLMKEWNIWNEIPIDDVSAFGDAESLTPLHLC VLGAHPKTTEVLLQSLDPNVKLKSSSLLHLATEWNNYPLLHVLLSSKRFDINYQDNELHE TPLYLACRLNFFEAAVCLLYNGADLEIREKLFGWTAIFVAAAEGFTDIVKLLIANNANFD IEDEGGWTPMEHAVLRGHLHIADMVQIRDELVTHPHSQLNSGSEEKEPLNEISAGELNER NENGNGGNKGSLGKLAGPIKSYGHRFLDNNESLILITLGSNDTRNKSPSISLSSEALAKV IGLETDCALSLVISCNDSIDKSSVILDLPLDDNVDAVDFKVPFKVDYSHTLYFDIVPTYG TRSLETHNRIDCQKNNNNYVMARGVSMLNKSYSSVGVNRSILNGSVTVPIIANHTLEILG TLKFEYIIITPFEHPQLPLERTETYWKSLVSTRVIGHRGLGKNNPNKSLQIGENTVESFI MAASLGASYVEFDVQLTKDNVPVVYHDFLVAETGVDIPMHELTLEQFLDLNNADKEHIQR GAGHSPHHVNGADTALQKYRGRSVDDSDVSTLRRAWDLHDNDPNGKSNNAHWSDNRMRLT KTFKKNNFKGNARGHSIASSFVTLKELFKKIPANVGFNIECKFPMLDEAEEEELGQIMME MNHWVDTVLKVVFDNANGRDIIFSSFHPDICIMLSLKQPVIPILFLTEGGSEQMADLRAS SLQNGIRFAKKWNLLGIVSAAAPILKAPRLVQVVKSNGLVCVTYGVDNNDPENASIQIEA GVDAVIVDSVLAIRRGLTKKNEK

References

External Links

Resource	Link
Saccharomyces Genome Database	GDE1
Uniprot ID	Q02979
Uniprot Name	GDE1_YEAST
GenBank Gene ID	U43503
Genebank Protein ID	1163103

General Reference

Bussey, H., Storms, R. K., Ahmed, A., Albermann, K., Allen, E., Ansorge, W., Araujo, R., Aparicio, A., Barrell, B., Badcock, K., Benes, V., Botstein, D., Bowman, S., Bruckner, M., Carpenter, J., Cherry, J. M., Chung, E., Churcher, C., Coster, F., Davis, K., Davis, R. W., Dietrich, F. S., Delius, H., DiPaolo, T., Hani, J., et, a. l. .. (1997). "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Nature 387:103-105.9169875
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., O'Shea, E. K. (2003). "Global analysis of protein localization in budding yeast." Nature 425:686-691.14562095
Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., Weissman, J. S. (2003). "Global analysis of protein expression in yeast." Nature 425:737-741.14562106
Fisher, E., Almaguer, C., Holic, R., Griac, P., Patton-Vogt, J. (2005). "Glycerophosphocholine-dependent growth requires Gde1p (YPL110c) and Git1p in Saccharomyces cerevisiae." J Biol Chem 280:36110-36117.16141200
Fernandez-Murray, J. P., McMaster, C. R. (2005). "Glycerophosphocholine catabolism as a new route for choline formation for phosphatidylcholine synthesis by the Kennedy pathway." J Biol Chem 280:38290-38296.16172116
Smolka, M. B., Albuquerque, C. P., Chen, S. H., Zhou, H. (2007). "Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Proc Natl Acad Sci U S A 104:10364-10369.17563356
Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., Zhou, H. (2008). "A multidimensional chromatography technology for in-depth phosphoproteome analysis." Mol Cell Proteomics 7:1389-1396.18407956