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MetaCyc Pathway: L-serine biosynthesis
Inferred from experiment

Enzyme View:

Pathway diagram: L-serine biosynthesis

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisAmino Acids BiosynthesisProteinogenic Amino Acids BiosynthesisL-serine Biosynthesis

Some taxa known to possess this pathway include : Arabidopsis thaliana col, Escherichia coli K-12 substr. MG1655, Homo sapiens, Methanocaldococcus jannaschii, Rattus norvegicus

Expected Taxonomic Range: Archaea, Bacteria , Eukaryota

About This Pathway

Serine biosynthesis is a major metabolic pathway in Escherichia coli K-12. Its end product, L-serine, is not only used in protein synthesis, but also as a precursor for the biosynthesis of glycine, cysteine, tryptophan, and phospholipids. In addition, it directly or indirectly serves as a source of one-carbon units for the biosynthesis of various compounds.

Regulation of the pathway is mainly accomplished by feedback inhibition of the enzyme that catalyzes the first committed step, D-3-phosphoglycerate dehydrogenase. The second enzyme in the pathway, 3-phosphoserine aminotransferase, requires pyridoxal 5'-phosphate (PLP) as a cofactor and is also required for the biosynthesis of PLP itself. Thus the cell must ensure that the supply of PLP is adequate. Little biochemical work has been done on the final enzyme of the pathway, phosphoserine phosphatase.

Review: Stauffer, G., Regulation of Serine, Glycine, and One-Carbon Biosynthesis. Module, in [ECOSAL].

Serine Biosynthesis in Plants

Serine biosynthesis in plants proceeds by two pathways, the so called phosphorylated pathway and the glycolate pathway. In the phosphorylated pathway (depicted here), serine is derived from 3-phosphoglycerate, an intermediate of glycolysis. This pathway also operates in bacteria, yeast, and animals. In the glycolate pathway, which is part of photorespiration ( photorespiration), serine is derived from glycolate via glycine. The glycolate pathway dominates in the photosynthetic tissues. Most of the serine produced in this pathway continues with the photorespiration pathway and is returned to Calvin cycle via hydroxypyruvate and glycerate. The phosphorylated pathway is thought to contribute to serine biosynthesis in the dark and in non-photosynthetic tissues. Genes of the phosphorylated pathway are upregulated by high salinity, flood and cold. It indicates that the phosphorylated pathway is also important in supplying serine under environmental stresses.

Citations: [Ho01]

Superpathways: superpathway of L-serine and glycine biosynthesis I, superpathway of sulfate assimilation and cysteine biosynthesis

Unification Links: AraCyc:SERSYN-PWY, EcoCyc:SERSYN-PWY

Created 08-Jul-1994 by Riley M, Marine Biological Laboratory


ECOSAL: EcoSal "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Ho01: Ho CL, Saito K (2001). "Molecular biology of the plastidic phosphorylated serine biosynthetic pathway in Arabidopsis thaliana." Amino Acids 20(3);243-59. PMID: 11354602

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Achouri97: Achouri Y, Rider MH, Schaftingen EV, Robbi M (1997). "Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase." Biochem J 323 ( Pt 2);365-70. PMID: 9163325

AlRabiee96: Al-Rabiee R, Zhang Y, Grant GA (1996). "The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Site-directed mutagenesis of effector binding site residues." J Biol Chem 271(38);23235-8. PMID: 8798520

Baek00: Baek JY, Jun DY, Taub D, Kim YH (2000). "Assignment of human 3-phosphoglycerate dehydrogenase (PHGDH) to human chromosome band 1p12 by fluorescence in situ hybridization." Cytogenet Cell Genet 89(1-2);6-7. PMID: 10894924

Baek03: Baek JY, Jun DY, Taub D, Kim YH (2003). "Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis." Biochem J 373(Pt 1);191-200. PMID: 12633500

Bell02: Bell JK, Pease PJ, Bell JE, Grant GA, Banaszak LJ (2002). "De-regulation of D-3-phosphoglycerate dehydrogenase by domain removal." Eur J Biochem 269(17);4176-84. PMID: 12199695

Bell04: Bell JK, Grant GA, Banaszak LJ (2004). "Multiconformational states in phosphoglycerate dehydrogenase." Biochemistry 43(12);3450-8. PMID: 15035616

Burton08: Burton RL, Hanes JW, Grant GA (2008). "A stopped flow transient kinetic analysis of substrate binding and catalysis in Escherichia coli D-3-phosphoglycerate dehydrogenase." J Biol Chem 283(44);29706-14. PMID: 18776184

Burton09: Burton RL, Chen S, Xu XL, Grant GA (2009). "Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding." Biochemistry 48(51);12242-51. PMID: 19924905

Cho00: Cho HM, Jun DY, Bae MA, Ahn JD, Kim YH (2000). "Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene." Gene 245(1);193-201. PMID: 10713460

Clarke73: Clarke SJ, Low B, Konigsberg WH (1973). "Close linkage of the genes serC (for phosphohydroxy pyruvate transaminase) and serS (for seryl-transfer ribonucleic acid synthetase) in Escherichia coli K-12." J Bacteriol 113(3);1091-5. PMID: 4570768

Collet97: Collet JF, Gerin I, Rider MH, Veiga-da-Cunha M, Van Schaftingen E (1997). "Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate." FEBS Lett 408(3);281-4. PMID: 9188776

Collet98: Collet JF, Stroobant V, Pirard M, Delpierre G, Van Schaftingen E (1998). "A new class of phosphotransferases phosphorylated on an aspartate residue in an amino-terminal DXDX(T/V) motif." J Biol Chem 273(23);14107-12. PMID: 9603909

Collet99: Collet JF, Stroobant V, Van Schaftingen E (1999). "Mechanistic studies of phosphoserine phosphatase, an enzyme related to P-type ATPases." J Biol Chem 274(48);33985-90. PMID: 10567362

Dey07: Dey S, Hu Z, Xu XL, Sacchettini JC, Grant GA (2007). "The effect of hinge mutations on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase." J Biol Chem 282(25);18418-26. PMID: 17459882

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Drewke96: Drewke C, Klein M, Clade D, Arenz A, Muller R, Leistner E (1996). "4-O-phosphoryl-L-threonine, a substrate of the pdxC(serC) gene product involved in vitamin B6 biosynthesis." FEBS Lett 1996;390(2);179-82. PMID: 8706854

Dubrow77: Dubrow R, Pizer LI (1977). "Transient kinetic studies on the allosteric transition of phosphoglycerate dehydrogenase." J Biol Chem 1977;252(5);1527-38. PMID: 320209

Duncan86: Duncan K, Coggins JR (1986). "The serC-aro A operon of Escherichia coli. A mixed function operon encoding enzymes from two different amino acid biosynthetic pathways." Biochem J 1986;234(1);49-57. PMID: 3518706

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Showing only 20 references. To show more, press the button "Show all references".

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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