PathwayMap:GlycerolipidBiosynthesis

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[title] <2.5,2.5> #Glycerolipid Metabolome de novo pathway of glycerophospholipid //titles [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 [ER] <6,113.5>css(font-size:40px;background:rgb(200,200,150;border:5px solid black;z-index:2) 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) //Mitochondria inner membrane [IMM] <57.5,17.5,1500,350>css(background:rgb(255,200,50;z-index:2;border:30px solid rgb(155,100,10) //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 [G3P3] <29.5,1.5> !GL{OH |OH|O-PO_s3s_} ?[link](http://lipidbank.jp/cgi-bin/main.cgi?id=PGP "G3P") d=(l_w5)=>u[LPA] d=(l_w5)=>u[LPAmt] //lysophosphatidic acid [LPA] <22.5,13> !GL{O-CO-R1|OH|O-PO_s3s_} LPA d=(l_w5)=>u[PAER] //lysophosphatidic acid [LPAmt] <36.5,13> !GL{O-CO-R1|OH|O-PO_s3s_} LPA d=(l_w5)=>u[PA2] //phosphatidic acid, mitochondrial [PAER] <23,32> !GL{O-CO-R1|O-CO-R2|O-PO_s3s_} ?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPA"PA") d=(l_w5)=>u[DAG2] d=(l_w5)=>u[CDP-DAGer] //phosphatidic acid, mitochondrial [PAmt] <54,15> !GL{O-CO-R1|O-CO-R2|O-PO_s3s_} ?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPA"PA") r=(l_w5)=>l[CDP-DAG] //cytidine diphosphate-diacylglycerol [CDP-DAG] <73,15> !GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>} CDP-DAG r=(l_w5)=>l[PGP] //cytidine diphosphate-diacylglycerol [CDP-DAGer] <22,60> !GL{O-CO-R1 | O-CO-R2 | O-PO2-CMP</t>} CDP-DAG 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 [PGP] <96,14> !PG{O-CO-R1 | O-CO-R2 | O-PO2-O| HO|O3P-O} PGP r=(l_w4)=>l[PG] //glycerol-3-phosphate [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 } ?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPG"PG") r=(l_w4)=>[CL] [H2O] <109,14> H2O 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 [CL] <138,12> !CL{O-CO-R1|O-CO-R2|O-PO-O|HO|O-PO-O|O-CO-R3| O-CO-R4} CL u=(l_w5)=>d[CL2] [CL2] <142,3> CL [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] [unknown] <53,38> ? u==>d[DAG] //diacylglycerol [DAG2] <22,48.5> !GL{O-CO-R1|O-CO-R1| OH} DAG r=(l_w5)=>[PC] //phosphatidylinositol [PI] <33.5,76> !GL{O-CO-R1 | O-CO-R2 | O-PO2-Inositol} ?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPI"PI") //phosphatidylinositol [PI2] <21.5,76> !GL{O-CO-R1 | O-CO-R2 | O-PO2-Inositol} ?[link](http://jcbl.jp/wiki/Volatile:ListMol?my_1=LBGPI"PI") //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") //phosphatidylethanolamine [PE] <24,92.5> !GL{O-CO-R1|O-CO-R2| O-PO2-Ethanolamine} PE //===================================Gene==================================================== [Tam41] <66,17>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) Tam41 <pop> 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> //phosphatidylglycerolphosphate (PGP) synthase [aa] (gene) <87,16.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) PGS1 //phosphatidylglycerophosphatase [PTPMT1] <109.5,17.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) PTPMT1 //cardiolipin synthase [CRLS1] <130.5,17>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) CRLS1 [PRELITRIAP1] <45.5,21>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) Transferred by PRELI1 + TRIAP1 <pop> <nobr>In yeast Ups1 shuffles PA between the OMM and IMM and the PA-loaded Ups1 needs the interaction with Mdm35 for stabilisation. ?[link](http://science.sciencemag.org/cgi/pmidlookup?view=long&pmid=23042293"Connerth et al. 2012. Science. 338(6108):815-818.") 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> //nucleoside diphosphate kinase Nm23-H4 [NME4] <139.5,7>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) Transffered by 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> //acylglycerol kinase [AGK] <56.5,24>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) AGK <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.") AGK deficiency results in Sengers syndrome with dysfunction of the mitochondrial energy metabolism. ?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3523805/"Calvo et al. 2012. Sci Transl Med. 4(118):118ra10.") ?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276657/"Mayr et al. 2012. Am J Hum Genet. 90(2):314-320.") </pop> [GPATer] <24.5,9>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) GPAT3,4 [GPATmit] <35.5,9>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) GPAT1,2 [AGPAT] <36.5,20>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) AGPAT1,4 [AGPAT2] <22,24>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) AGPAT1,2,3,5 //Phosphatidate phosphatase [LPIN] <23,42.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) LPIN ?[link](http://www.genome.jp/dbget-bin/www_bget?ec:3.1.3.4"KEGG") <pop> Phosphatidate phosphatase </pop> //CDP-diacylglycerol--inositol 3-phosphatidyltransferase [CDIPT] <36.5,69>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) CDIPT ?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.11"KEGG") //CDP-diacylglycerol--inositol 3-phosphatidyltransferase [CDIPT2] <24,69>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) CDIPT ?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.11"KEGG") //Cholinephosphotransferase [CHPT1] <44,48.5>css(background:rgb(255,200,50;border:5px solid rgb(255,100,50;z-index:5) CHPT ?[link](http://www.genome.jp/dbget-bin/www_bget?ec:2.7.8.2"KEGG") ?[link](http://www.uniprot.org/uniprot/Q8WUD6"UniProt") <pop> <nobr>Subcellular localization ?[link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC124149/"Henneberry et al.( 2002) Mol Biol Cell. 13(9):3148-3161") </pop>