PathwayMap:GlycerolipidBiosynthesis: Difference between revisions

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#Glycerolipid Metabolome
#Glycerolipid Metabolome
de novo pathway of glycerophospholipid
de novo pathway of glycerophospholipid
//Glycerol-3-phosphate acyltransferase
g[GPAM]
GPAT
<span>
Protein
Glycerol-3-phosphate acyltransferase
<br>
Subcellular location
GPAT1,2:Mitochondrion
GPAT3,4:ER
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.3.1.15"KEGG")


UniPlot <a href=http://www.uniprot.org/uniprot/Q9SHJ5>1</a>, <a href=http://www.uniprot.org/uniprot/Q9SHJ5>2</a>, <a href=http://www.uniprot.org/uniprot/Q9SHJ5>3</a>, <a href=http://www.uniprot.org/uniprot/Q9SHJ5>4</a>
//titles
</span>
[OMM_name] <88.5,42.5>css(font-size:40px;background:rgb(200,200,150;border:5px solid black;color:)
Mitochondrial outer membrane


[IMM_name] <88.5,35>css(font-size:40px;background:rgb(200,200,150;border:5px solid black;color:)
Mitochondrial inner membrane


[ERtext] (trans) <45.5,77.5>css(font-size:50px)
Endoplasmic Reticulum


[MTtext] (trans) <54,29.5>css(font-size:50px)
[ER] <6,113.5>css(font-size:40px;background:rgb(200,200,150;border:5px solid black;z-index:2)
Mitochondrion
Endoplasmic reticulum


//=========================================Organelles======================================================
//Mitochondria outer membrane
[OMM] <38.5,2.5,2100,700>css(background:rgb(255,200,50;z-index:1;border:30px solid rgb(155,100,10)


[ER] <2,3,350,1352>css(background:rgb(0,200,50 ; color:black; border-:100px;  box-shadow:none;z-index:1;)
//Mitochondria inner membrane
ER
[IMM] <57.5,17.5,1500,350>css(background:rgb(255,200,50;z-index:2;border:30px solid rgb(155,100,10)
 
[ER2] <22,37.5,1000,800>css(background:rgb(0,200,50;  box-shadow:none;z-index:0;)
 
 
[MT] <25,3,950,540>css(background:rgb(255,200,50 ; border-:100px;  box-shadow:none;z-index:1;)


//Endoplasmic reticulum
[ER1] <1,1,400,2050>css(background:rgb(200,255,10;border-right:50px solid rgb(200,200,0;box-shadow:none;z-index:1)




//Golgi
[Golgi] <39,51.5,700,1000>css(background:rgb(50,140,140;border:30px solid rgb(100,200,200;box-shadow:none;z-index:1)




//=========================================Metabolites=====================================================
//glycerol-3-phosphate
//glycerol-3-phosphate
[G3P] <9,8>
[G3P3] <29.5,1.5>
!GL{OH |OH|O-PO_s3s_}
!GL{OH |OH|O-PO_s3s_}
?[link](http://lipidbank.jp/cgi-bin/main.cgi?id=PGP "G3P")
?[link](http://lipidbank.jp/cgi-bin/main.cgi?id=PGP "G3P")
<pop>
d=(l_w5)=>u[LPA]
//![image](img/G3P.png)
d=(l_w5)=>u[LPAmt]
glycerol-3-phosphate
 
</pop>
d=[GPAM](l_w3)=>u[LPA]


//lysophosphatidic acid
//lysophosphatidic acid
[LPA] <8,21.5>
[LPA] <22.5,13>
!GL{O-CO-R1|OH|O-PO_s3s_}
!GL{O-CO-R1|OH|O-PO_s3s_}
LPA
LPA
<pop>
d=(l_w5)=>u[PAER]
lysophosphatidic acid


</pop>
//lysophosphatidic acid
d=[AGPAT](l_w3)=>u[PA]
[LPAmt] <36.5,13>
!GL{O-CO-R1|OH|O-PO_s3s_}
LPA
d=(l_w5)=>u[PA2]




//phosphatidic acid
//phosphatidic acid, mitochondrial
[PA] <8,32>
[PAER] <23,32>
!GL{O-CO-R1|O-CO-R1|O-PO_s3s_}
!GL{O-CO-R1|O-CO-R2|O-PO_s3s_}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPA"PA")
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPA"PA")
d=[LPIN](l_w3)=>u[DAG]
d=(l_w5)=>u[DAG2]
r=[CDS2](l_w3)=>l[CDP-DAG]
d=(l_w5)=>u[CDP-DAGer]
r=[CDS1](l_w3)=>[CDP-DAGer]


 
//phosphatidic acid, mitochondrial
//diacylglycerol
[PAmt] <54,15>
[DAG] <7.5,58.5>
!GL{O-CO-R1|O-CO-R2|O-PO_s3s_}
!GL{O-CO-R1|O-CO-R1| OH}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPA"PA")
DAG
r=(l_w5)=>l[CDP-DAG]
=[CHPT1](l_w3)=>[PC]
=[CEPT1SELENOI](l_w3)=>[PE]


//cytidine diphosphate-diacylglycerol
//cytidine diphosphate-diacylglycerol
[CDP-DAG] <27.5,26>
[CDP-DAG] <73,15>
!GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>}
!GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>}
CDP-DAG
CDP-DAG
u=[PGS1](l_w3)=>d[PGP]
r=(l_w5)=>l[PGP]
 


//cytidine diphosphate-diacylglycerol
//cytidine diphosphate-diacylglycerol
[CDP-DAGer] <28.5,39>
[CDP-DAGer] <22,60>
!GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>}
!GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>}
CDP-DAG
CDP-DAG
r=[CDIPT](l_w3)=>[PI]
r=(l_w5)=>u[PI]
d=(l_w5)=>u[PI2]
//cytidine triphosphate
[CTP] <64,14.5>
CTP
d=(l_w2)=>d[PPi]


//pyrophosphate
[PPi] <68.5,13>
pyrophosphate


//phosphatidylglycerol-phosphate
//phosphatidylglycerol-phosphate
[PGP] <27.5,9.5>
[PGP] <96,14>
!PG{O-CO-R1 | O-CO-R2 | O-PO2-O| HO|O3P-O}
!PG{O-CO-R1 | O-CO-R2 | O-PO2-O| HO|O3P-O}
PGP
PGP
=[PTPMT1] (l_w3)=>[PG]
r=(l_w4)=>l[PG]


//phosphatidylglycerol
//glycerol-3-phosphate
[PG] <49,9.5>
[G3P] <82.5,9>
!GL{OH |OH|O-PO_s3s_}
?[link](http://lipidbank.jp/cgi-bin/main.cgi?id=PGP "G3P")
d=(l_w2)=>d[CMP]
 
[CMP] <90.5,13>
CMP
 
[PG] <118,13.5>
!PG{O-CO-R1 | O-CO-R2 | PO2-O| HO|HO }
!PG{O-CO-R1 | O-CO-R2 | PO2-O| HO|HO }
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPG"PG")
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPG"PG")
=[CRLS1](l_w3)=>[CL]


//phosphatidylinositol
r=(l_w4)=>[CL]
[PI] <48,38.5>
[H2O] <109,14>
!GL{O-CO-R1 | O-CO-R2 | O-PO2-Inositol}
H2O
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPI"PI")
d=(l_w2)=>d[Pi]
 
[Pi] <113,14>
Pi
 
[CDP-DAGbox] <128,13.5>
CDP-DAG
d=(l_w2)=>d[CMP2]
 
[CMP2] <134.5,13.5>
CMP


//cardiolipin
//cardiolipin
[CL] <70.5,8>
[CL] <138,12>
!CL{O-CO-R1|O-CO-R2|O-PO-O|HO|O-PO-O|O-CO-R3| O-CO-R4}
!CL{O-CO-R1|O-CO-R2|O-PO-O|HO|O-PO-O|O-CO-R3| O-CO-R4}
CL
CL
u=(l_w5)=>d[CL2]


//phosphatidylcholine
[CL2] <142,3>
[PC] <26.5,51>
CL
!GL{O-CO-R1|O-CO-R1|O-PO2-Choline}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPC"PC")


d=[PTDSS](l_w3)=>u[PS]
[PA2] <37,23.5>
!GL{O-CO-R1|O-CO-R2|O-PO_s3s_}
PA
=(l_w5)=>[PAmt]


//diacylglycerol
[DAG] <54,28>
!GL{O-CO-R1|O-CO-R1| OH}
DAG
u=(l_w5)=>d[PAmt]


//phosphatidylethanolamine
[unknown] <53,38>
[PE] <25,75>
?
!GL{O-CO-R1|O-CO-R1| O-PO2-Ethanolamine}
u==>d[DAG]
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPE "PE")
u=[PTDSS]l(l_w3)=>d[PS]


//phosphatidylserine
//diacylglycerol
[PS] (box) <26.5,62.5>
[DAG2] <22,48.5>
!GL{O-CO-R1|O-CO-R1|O-PO2-Serine}
!GL{O-CO-R1|O-CO-R1| OH}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPS "PS")
DAG
d=[PISD]r(l_w3)=>u[PE]  
r=(l_w5)=>[PC]


//1-acylglycerol-3-phosphate O-acyltransferase
//phosphatidylinositol
g[AGPAT]
[PI] <33.5,76>
AGPAT
!GL{O-CO-R1 | O-CO-R2 | O-PO2-Inositol}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPI"PI")


//Phosphatidate cytidylyltransferase
//phosphatidylinositol
g[CDS2]
[PI2] <21.5,76>
CDS2
!GL{O-CO-R1 | O-CO-R2 | O-PO2-Inositol}
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.7.41"KEGG")
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPI"PI")


//Phosphatidate cytidylyltransferase
g[CDS1]
CDS1
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.7.41"KEGG")


//phosphatidylcholine
[PC] <53.5,48.5>
!GL{O-CO-R1|O-CO-R2|O-PO2-Choline}
?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPC"PC")


//CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
//phosphatidylethanolamine
g[PGS1]
[PE] <24,92.5>
PGS
!GL{O-CO-R1|O-CO-R2| O-PO2-Ethanolamine}
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.5 "KEGG")
PE


//Phosphatidylglycerophosphatase
//===================================Gene====================================================
g[PTPMT1]
[Tam41] <66,17>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
PTPMT
Tam41
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:3.1.3.27"KEGG")


//cardiolipin synthase
g[CRLS1]
CRLS
?[link](http://www.uniprot.org/uniprot/Q9UJA2"UniProt")
//Phosphatidate phosphatase
g[LPIN]
LPIN
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:3.1.3.4"KEGG")
<pop>
<pop>
Phosphatidate phosphatase
Enzyme: CDP-diacylglycerol synthase<br>
<nobr>This reaction is not catalyzed by Cds1 in mitochondria.
?[link](http://www.cell.com/cell-metabolism/pdf/S1550-4131(13)00142-3.pdf"Tamura et al. 2013. Cell Metab. 17(5):709-718.")
</pop>
</pop>


//Cholinephosphotransferase
//phosphatidylglycerolphosphate (PGP) synthase
g[CHPT1]
[aa] (gene) <87,16.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CHPT
PGS1
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.2"KEGG")
?[link](http://www.uniprot.org/uniprot/Q8WUD6"UniProt")


//Ethanolaminephosphotransferase 1
//phosphatidylglycerophosphatase
g[CEPT1SELENOI]
[PTPMT1] <109.5,17.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CEPT1/SELENOI
PTPMT1
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.1"KEGG")


//cardiolipin synthase
[CRLS1] <130.5,17>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CRLS1


//Phosphatidylserine synthase
[PRELITRIAP1] <45.5,21>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
g[PTDSS]
Transferred by
PTDSS
PRELI1 + TRIAP1
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.8"KEGG")


//Phosphatidylserine decarboxylase
<pop>
g[PISD]
<nobr>In yeast Ups1  shuffles PA between the OMM and IMM and the PA-loaded Ups1 needs the interaction with Mdm35 for stabilisation.
PISD
?[link](http://science.sciencemag.org/cgi/pmidlookup?view=long&pmid=23042293"Connerth et al. 2012. Science. 338(6108):815-818.")
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:4.1.1.65"KEGG")
In human, the orthologous gene of  Ups1 is PRELI1 and TRIAP1 is the gene which has the function of Mdm35.
?[link](https://linkinghub.elsevier.com/retrieve/pii/S1550-4131(13)00297-0"Potting et al. 2013. Cell Metab. 18(2):287-295.")
</pop>


//CDP-diacylglycerol--inositol 3-phosphatidyltransferase
//nucleoside diphosphate kinase Nm23-H4
g[CDIPT]
[NME4] <139.5,7>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CDIPT
Transffered by
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.11"KEGG")
Nm23-H4
<pop>
<nobr>The nucleoside diphosphate kinase Nm23-H4 (encoded by the NME4 gene) localizes in the mitochondrial inter-membrane space
and seems to have a dual function either in the transfer of phosphate groups or in the transfer of CL from the IMM to the OMM.
?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23150663/"Schlattner et al. 2013. J Biol Chem. 288(1):111-121.")
</pop>


//Inositol
//acylglycerol kinase
[Inositol] <38,44.5>
[AGK] <56.5,24>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
Inositol
AGK
u==>u[CMP]
<pop>
<nobr>There is a term "Multi-substrate lipid kinase (MuLK)" (Waggoner et al., 2004).
This enzyme phosphorylates diacylglycerol, ceramide, and 1-acylglycerol but not sphingosine.
?[link](http://www.jbc.org/content/279/37/38228.long"Waggoner et al. 2004. J Biol Chem. 279(37):38228-38235.")


//Inositol
AGK deficiency results in Sengers syndrome with dysfunction of the mitochondrial energy metabolism.
[CMP] <45,44.5>
CMP


//CTP
?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523805/"Calvo et al. 2012. Sci Transl Med. 4(118):118ra10.")
[CTP] <17.5,29>
?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276657/"Mayr et al. 2012. Am J Hum Genet. 90(2):314-320.")
CTP
d==>d[PPi]


//PPi
</pop>
[PPi] <22,27>
PPi


//H2O
[GPATer] <24.5,9>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
[H2O] <7,43.5>
GPAT3,4
H2O
r==>r[Pi]


//Pi
[GPATmit] <35.5,9>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
[Pi] <8,50.5>
GPAT1,2
Pi


//CDP-Ethanolamine
[AGPAT] <36.5,20>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
[CDPethanolamine] <8.5,66>
AGPAT1,4
CDP-Ethanolamine
r==>r[CMP2]


//CMP
[AGPAT2] <22,24>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
[CMP2] <14.5,72>
AGPAT1,2,3,5
CMP


//CDP-Choline
//Phosphatidate phosphatase
[CDPcholine] <12.5,55>
[LPIN] <23,42.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CDP-Choline
LPIN
r==>l[CMP3]
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:3.1.3.4"KEGG")
<pop>
Phosphatidate phosphatase
</pop>


//CMP
//CDP-diacylglycerol--inositol 3-phosphatidyltransferase
[CMP3] <24.5,59.5>
[CDIPT] <36.5,69>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CMP
CDIPT
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.11"KEGG")


//Serine
[Serine] <34.5,57.5>
Ser
l==>l[Choline]


//Choline
//CDP-diacylglycerol--inositol 3-phosphatidyltransferase
[Choline] <34.5,60.5>
[CDIPT2] <24,69>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
Choline
CDIPT
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.11"KEGG")


//CMP4
//Cholinephosphotransferase
[CMP4] <66,16.5>
[CHPT1] <44,48.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5)
CMP
CHPT
?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.2"KEGG")
?[link](http://www.uniprot.org/uniprot/Q8WUD6"UniProt")


//CDP-DAG---CL
<pop>
[conect1] <59,16.5>
<nobr>Subcellular localization
CDP-DAG
?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124149/"Henneberry et al.( 2002) Mol Biol Cell. 13(9):3148-3161")
d=(l_w3)=r[CDP-DAG]
</pop>
u=(l_w3)=>u[CMP4]
 
//H2O2
[H2O2] <40,10.5>
H2O
d==>d[Pi2]
 
//Pi2
[Pi2] <44.5,10.5>
Pi
 
//glycerophosphate
[glycerophosphate] <34.5,23.5>
glycerophosphate
 
l==>[CMP5]
 
//CMP5
[CMP5] <34.5,20>
CMP


</nowiki>
</nowiki>
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Latest revision as of 05:29, 29 November 2023

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