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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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Escherichia coli K-12 substr. MG1655 Pathway: serine biosynthesis

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Genetic Regulation Schematic: ?

Superclasses: Biosynthesis Amino Acids Biosynthesis Individual Amino Acids Biosynthesis Serine Biosynthesis

Summary:
Serine biosynthesis is a major metabolic pathway in E. coli. Its end product, 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 / α-ketoglutarate reductase. The second enzyme in the pathway, 3-phosphoserine aminotransferase, requires pyridoxal 5'-phosphate as a cofactor and is also required for the biosynthesis of pyridoxal 5'-phosphate itself. Thus the cell must ensure that the supply of pyridoxal 5'-phosphate 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 3.6.1.2, [ECOSAL]

Citations: [Smallbone13]

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

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


References

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

Smallbone13: Smallbone K, Stanford NJ (2013). "Kinetic modeling of metabolic pathways: application to serine biosynthesis." Methods Mol Biol 985;113-21. PMID: 23417802

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

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

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

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

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

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Grant00: Grant GA, Xu XL, Hu Z (2000). "Removal of the tryptophan 139 side chain in Escherichia coli D-3-phosphoglycerate dehydrogenase produces a dimeric enzyme without cooperative effects." Arch Biochem Biophys 375(1);171-4. PMID: 10683264

Grant00a: Grant GA, Xu XL, Hu Z (2000). "Role of an interdomain Gly-Gly sequence at the regulatory-substrate domain interface in the regulation of Escherichia coli. D-3-phosphoglycerate dehydrogenase." Biochemistry 39(24);7316-9. PMID: 10852732

Grant01: Grant GA, Hu Z, Xu XL (2001). "Specific interactions at the regulatory domain-substrate binding domain interface influence the cooperativity of inhibition and effector binding in Escherichia coli D-3-phosphoglycerate dehydrogenase." J Biol Chem 276(2);1078-83. PMID: 11050089

Grant01a: Grant GA, Hu Z, Xu XL (2001). "Amino acid residue mutations uncouple cooperative effects in Escherichia coli D-3-phosphoglycerate dehydrogenase." J Biol Chem 276(21);17844-50. PMID: 11278587

Grant02: Grant GA, Hu Z, Xu XL (2002). "Cofactor binding to Escherichia coli D-3-phosphoglycerate dehydrogenase induces multiple conformations which alter effector binding." J Biol Chem 277(42);39548-53. PMID: 12183470

Grant03: Grant GA, Hu Z, Xu XL (2003). "Hybrid tetramers reveal elements of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase." J Biol Chem 278(20);18170-6. PMID: 12644455

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Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc12.