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actions-user committed Oct 9, 2024
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2 changes: 1 addition & 1 deletion pathways/WP128/WP128-bibliography.tsv
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ID Database Citation
9409150 Pubmed "Thomas D, Surdin-Kerjan Y. Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1997 Dec;61(4):503–32. <a href=""http://www.ncbi.nlm.nih.gov/pubmed/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"
9409150 Pubmed "Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Thomas D, Surdin-Kerjan Y. Microbiol Mol Biol Rev. 1997 Dec;61(4):503–32. <a href=""http://www.ncbi.nlm.nih.gov/pubmed/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">PubMed</a> <a href=""https://europepmc.org/abstract/MED/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">Europe PMC</a> <a href=""https://scholia.toolforge.org/pubmed/9409150"" target=""_blank"" class=""external"" rel=""nofollow"">Scholia</a>"
8 changes: 4 additions & 4 deletions pathways/WP128/WP128-datanodes.tsv
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Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI PubChem ChemSpider HMDB KEGG LipidMaps
L-cysteine Metabolite cas:52-90-4 "" wikidata:Q106345475;wikidata:Q186474 chebi:17561;chebi:35235 inchikey:XUJNEKJLAYXESH-REOHCLBHSA-N pubchem.compound:5862 chemspider:5653 hmdb:HMDB0000574 kegg.compound:C00097
L-serine Metabolite cas:56-45-1 "" wikidata:Q106345473;wikidata:Q183290 chebi:33384;chebi:17115 inchikey:MTCFGRXMJLQNBG-REOHCLBHSA-N pubchem.compound:5951;pubchem.compound:6857581 chemspider:5736 hmdb:HMDB0000187 kegg.compound:C00065
homocysteine Metabolite cas:6027-13-0 "" wikidata:Q26992833;wikidata:Q106345493 chebi:58199;chebi:17588 inchikey:FFFHZYDWPBMWHY-VKHMYHEASA-N pubchem.compound:6971015;pubchem.compound:91552 chemspider:82666 hmdb:HMDB0000742 kegg.compound:C00155
cystathionine Metabolite cas:56-88-2 "" wikidata:Q28529685;wikidata:Q106345609 chebi:58161;chebi:17482 inchikey:ILRYLPWNYFXEMH-WHFBIAKZSA-N pubchem.compound:439258;pubchem.compound:25243997 chemspider:16735760;chemspider:388392 hmdb:HMDB0000099 kegg.compound:C02291
L-serine Metabolite cas:56-45-1 "" wikidata:Q106345473;wikidata:Q183290 chebi:33384;chebi:17115 inchikey:MTCFGRXMJLQNBG-REOHCLBHSA-N pubchem.compound:5951;pubchem.compound:6857581 chemspider:5736 hmdb:HMDB0000187 kegg.compound:C00065
L-cysteine Metabolite cas:52-90-4 "" wikidata:Q106345475;wikidata:Q186474 chebi:17561;chebi:35235 inchikey:XUJNEKJLAYXESH-REOHCLBHSA-N pubchem.compound:5862 chemspider:5653 hmdb:HMDB0000574 kegg.compound:C00097
acetate Metabolite cas:64-19-7 "" wikidata:Q47512 chebi:15366 inchikey:QTBSBXVTEAMEQO-UHFFFAOYSA-N pubchem.compound:176 chemspider:171 hmdb:HMDB0000042 kegg.compound:C00033 lipidmaps:LMFA01010002
STR3 GeneProduct sgd:S000003152 "" ensembl:YGL184C ncbigene:852691 uniprot:P53101
CYS4 GeneProduct sgd:S000003387 "" ensembl:YGR155W ncbigene:853059 uniprot:P32582
STR2 GeneProduct sgd:S000003891 "" ensembl:YJR130C ncbigene:853594 uniprot:P47164
CYS3 GeneProduct sgd:S000000010 "" ensembl:YAL012W ncbigene:851221 uniprot:P31373
CYS4 GeneProduct sgd:S000003387 "" ensembl:YGR155W ncbigene:853059 uniprot:P32582
STR3 GeneProduct sgd:S000003152 "" ensembl:YGL184C ncbigene:852691 uniprot:P53101
186 changes: 95 additions & 91 deletions pathways/WP128/WP128.gpml
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92 changes: 30 additions & 62 deletions pathways/WP128/WP128.json
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"author": "[M.Braymer, MaintBot, Christine Chichester, Egonw, DeSl, AlexanderPico, Eweitz]",
"author": "[M.Braymer, MaintBot, Christine Chichester, Egonw, DeSl, AlexanderPico, Eweitz, Khanspers]",
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"content": "The first five steps of arginine biosynthesis in S. cerevisiae take place in the mitochondrion (CITS: [11553611])(CITS: [Hinnebusch]). This part of the pathway is known as the acetylated derivatives cycle because the acetyl group that is added to L-glutamate in the first step of the pathway is recycled via N-acetylglutamate generated in the fifth step. The enzymes that catalyze the second and third steps are encoded by a single gene (ARG5,6) that is translated into a pre-protein which is imported into mitochondria and cleaved there to yield two enzymes, N-acetylglutamate kinase and N-acetylglutamyl-phosphate reductase (CITS: [1649049]). These enzymes form a complex with each other and with N-acetylglutamate synthase, the first enzyme in the pathway, which may have implications for regulation of their activity (CITS: [11553611]). The mitochondrial steps of the arginine biosynthesis pathway result in the formation of ornithine, which is exported to the cytoplasm by the transporter Ort1p (CITS: [8798783]). In the cytoplasm, L-ornithine is converted to L-arginine in three reactions mediated by ornithine carbamoyltransferase, arginosuccinate synthase, and argininosuccinate lyase. Transcription of genes of the arginine biosynthetic pathway, as well as of other amino acid biosynthetic pathways, is activated by the transcription factor Gcn4p under conditions of amino acid starvation (CITS: [11390663])(CITS: [Hinnebusch]). Transcription of ARG1, ARG3, ARG5,6, and ARG8 is also repressed in the presence of arginine by the ArgR/Mcm1p complex, which consists of Arg80p, Arg81p, Arg82p, and Mcm1p (CITS: [14563547]). The transcriptional activator Gcn4p interacts with subunits of the ArgR/Mcm1p repressor, allowing for fine-tuning of transcriptional control in response to arginine availability (CITS: [15289616]). \r\nSOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html",
"source": "WikiPathways-description"
"content": "Based on http://pathway.yeastgenome.org/biocyc/"
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{
"content": "Based on http://pathway.yeastgenome.org/biocyc/"
"content": "The metabolic interconversion of cysteine and homocysteine via formation of a cystathionine intermediate is known as the transsulfuration pathway. While the transsulfuration pathway proceeds in only one direction in many bacteria and fungi, S. cerevisiae encodes for both a forward and reverse version of the pathway and is able to convert cysteine and homocysteine to one or the other reversibly. In the forward pathway, cysteine reacts with O-acetylhomoserine in a reaction catalyzed by cystathionine -synthase to form cystathionine. Cystathionine is then cleaved by cystathionine -lyase, yielding pyruvate, ammonia, and homocysteine. In S. cerevisiae, cystathionine -synthase and -lyase are thought to be encoded by STR2 and STR3 respectively, due to their similarity to the aforementioned enzymes in other organisms and the inability of str2 or str3 null mutants to utilize cysteine as a sole sulfur source. In the reverse pathway, cystathionine -synthase (Cys4p) catalyzes the condensation of homocysteine and serine to form cystathionine. Cystathionine -lyase (Cys3p) then catalyzes hydrolysis of cystathionine to produce cysteine, -ketobutyrate, and ammonia.\r\n\r\nThe presence of two transsulfuration pathways in S. cerevisiae enables the cell to acquire methionine from cysteine and vice-versa by using homocysteine as an intermediate. Homocysteine derived from cysteine in the forward transsulfuration pathway can be converted to methionine, while homocysteine derived from methionine can be converted to cysteine via the reverse transsulfuration pathway. This enables S. cerevisiae to utilize methionine or cysteine as a sole source of sulfur.\r\n\r\nSource: https://pathway.yeastgenome.org/",
"source": "WikiPathways-description"
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Binary file modified pathways/WP128/WP128.png
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