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Escherichia coli K-12 substr. MG1655 Enzyme: 3-phosphoserine aminotransferase [multifunctional]



Gene: serC Accession Numbers: EG10946 (EcoCyc), b0907, ECK0898

Synonyms: pdxC, pdxF

Regulation Summary Diagram: ?

Regulation summary diagram for serC

Subunit composition of 3-phosphoserine aminotransferase [multifunctional] = [SerC]2

Summary:
The serC-encoded enzyme, phosphoserine/phosphohydroxythreonine aminotransferase, functions in the biosythesis of both serine and pyridoxine, by using different substrates [Lam90]. Pyridoxal 5'-phosphate is a cofactor for both enzyme activities, suggesting that it can act in an autocatalytic fashion, stimulating its own biosynthesis [Drewke96].

The redundancy and promiscuity among aminotransferase enzymes has been investigated. [Drewke96] stated that no activity could be observed with non-phosphorylated substrates; however, [Duncan86] was able to use 3-hydroxypyruvate as the substrate for an assay of SerC enzymatic activity. In addition, genetic experiments showed that SerC is a minor alanine transaminase [Kim10a, Yoneyama11].

The normal activities of two enzymes, ArgD and SerC, are sufficient for succinyldiaminopimelate (SDAP) and lysine biosynthesis; a third enzyme, AstC, is sufficient for SDAP biosynthesis, but alone can not fulfill the cell's requirement for lysine. Additional enzymes, including GabT and PuuE, may be able to contribute to SDAP biosynthesis. Expression of argD, astC, serC, aspC, gabT, hisC, ilvE, patA, puuE, or tyrB from a plasmid allow growth of the triple ΔargD serC astC mutant on minimal medium [Lal14].

Crystal structures of the enzyme in the unligated form and in complex with the substrate analog α-methyl-L-glutamate have been solved, and a molecular reaction mechanism was proposed [Hester99].

serC is essential for growth on glycerol minimal medium; the growth defect can be rescued by addition of serine and pyridoxol/pyridoxine [Joyce06, Sakai02, Ravnikar87, Clarke73].

Citations: [Wintermute10, Ivancic13, Smallbone13, Gu14]

Gene Citations: [Man97, Lim94]

Locations: cytosol

Map Position: [956,876 -> 957,964] (20.62 centisomes, 74°)
Length: 1089 bp / 362 aa

Molecular Weight of Polypeptide: 39.783 kD (from nucleotide sequence), 39 kD (experimental) [Duncan86 ]

Molecular Weight of Multimer: 79 kD (experimental) [Duncan86]

Unification Links: ASAP:ABE-0003093 , CGSC:171 , DIP:DIP-2896N , EchoBASE:EB0939 , EcoGene:EG10946 , EcoliWiki:b0907 , Mint:MINT-1249760 , ModBase:P23721 , OU-Microarray:b0907 , PortEco:serC , Pride:P23721 , Protein Model Portal:P23721 , RefSeq:NP_415427 , RegulonDB:EG10946 , SMR:P23721 , String:511145.b0907 , UniProt:P23721

Relationship Links: InterPro:IN-FAMILY:IPR000192 , InterPro:IN-FAMILY:IPR003248 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR020578 , InterPro:IN-FAMILY:IPR022278 , Panther:IN-FAMILY:PTHR21152:SF1 , PDB:Structure:1BJN , PDB:Structure:1BJO , Pfam:IN-FAMILY:PF00266 , Prosite:IN-FAMILY:PS00595

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for serC

GO Terms:

Biological Process: GO:0006563 - L-serine metabolic process Inferred from experiment [Saito97]
GO:0006564 - L-serine biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Clarke73]
GO:0033359 - lysine biosynthetic process via diaminopimelate and N-succinyl-2-amino-6-ketopimelate Inferred from experiment [Lal14]
GO:0042823 - pyridoxal phosphate biosynthetic process Inferred from experiment [Lam90]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0008615 - pyridoxine biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004648 - O-phospho-L-serine:2-oxoglutarate aminotransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Duncan86]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Drewke96]
GO:0042803 - protein homodimerization activity Inferred from experiment [Duncan86]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0008483 - transaminase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids serine

Essentiality data for serC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose No 37 Aerobic 7.2 0.22 No [Baba06, Comment 2]
No [Feist07, Comment 4]

Credits:
Last-Curated ? 15-Oct-2014 by Keseler I , SRI International


Enzymatic reaction of: 3-phosphoserine aminotransferase

Synonyms: phosphoserine aminotransferase, phosphoserine 2-keto-glutarate transaminase, O-phospho-L-serine:2-oxoglutarate aminotransferase, phosphoserine transaminase

EC Number: 2.6.1.52

3-phospho-L-serine + 2-oxoglutarate <=> 3-phospho-hydroxypyruvate + L-glutamate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

Alternative Substrates for 3-phospho-hydroxypyruvate: hydroxypyruvate [Duncan86 ]

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

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Drewke96]

Kinetic Parameters:

Substrate
Km (μM)
Citations
3-phospho-L-serine
17.0
[Drewke96]
3-phospho-hydroxypyruvate
15.0
[Drewke96]

pH(opt): 8.8 [Drewke96]


Enzymatic reaction of: phosphohydroxythreonine aminotransferase

Synonyms: phosphohydroxythreonine transaminase

EC Number: 2.6.1.52

2-oxo-3-hydroxy-4-phosphobutanoate + L-glutamate <=> 4-phospho-hydroxy-L-threonine + 2-oxoglutarate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

In Pathways: superpathway of pyridoxal 5'-phosphate biosynthesis and salvage , pyridoxal 5'-phosphate biosynthesis I

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Drewke96]

Kinetic Parameters:

Substrate
Km (μM)
Citations
4-phospho-hydroxy-L-threonine
110.0
[Drewke96]

pH(opt): 8.3 [Drewke96]


Enzymatic reaction of: N-succinyldiaminopimelate aminotransferase

EC Number: 2.6.1.17

2-oxoglutarate + N-succinyl-L,L-2,6-diaminopimelate <=> L-glutamate + N-succinyl-2-amino-6-ketopimelate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

This reaction is reversible.

In Pathways: aspartate superpathway , superpathway of L-lysine, L-threonine and L-methionine biosynthesis I , L-lysine biosynthesis I

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate


Sequence Features

Protein sequence of SerC with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97]
 
Chain 2 -> 362
[UniProt09]
UniProt: Phosphoserine aminotransferase;
Amino-Acid-Sites-That-Bind 9
[UniProt15]
UniProt: L-glutamate.
Amino-Acid-Sites-That-Bind 42
[UniProt15]
UniProt: L-glutamate.
Protein-Segment 76 -> 77
[UniProt10a]
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 102
[UniProt15]
UniProt: Pyridoxal phosphate.
Amino-Acid-Sites-That-Bind 153
[UniProt15]
UniProt: Pyridoxal phosphate.
Amino-Acid-Sites-That-Bind 174
[UniProt15]
UniProt: Pyridoxal phosphate.
Amino-Acid-Sites-That-Bind 197
[UniProt15]
UniProt: Pyridoxal phosphate.
N6-pyridoxal-phosphate-Lys-Modification 198
[UniProt15]
UniProt: N6-(pyridoxal phosphate)lysine.
Protein-Segment 239 -> 240
[UniProt10a]
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest;
Sequence-Conflict 293
[Duncan86, UniProt10]
UniProt: (in Ref. 1);


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b0907 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10946; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

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

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

Gu14: Gu P, Yang F, Su T, Li F, Li Y, Qi Q (2014). "Construction of an L-serine producing Escherichia coli via metabolic engineering." J Ind Microbiol Biotechnol 41(9);1443-50. PMID: 24997624

Hester99: Hester G, Stark W, Moser M, Kallen J, Markovic-Housley Z, Jansonius JN (1999). "Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 A resolution: comparison of the unligated enzyme and a complex with alpha-methyl-l-glutamate." J Mol Biol 286(3);829-50. PMID: 10024454

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Ivancic13: Ivancic T, Jamnik P, Stopar D (2013). "Cold shock CspA and CspB protein production during periodic temperature cycling in Escherichia coli." BMC Res Notes 6;248. PMID: 23815967

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim10a: Kim SH, Schneider BL, Reitzer L (2010). "Genetics and regulation of the major enzymes of alanine synthesis in Escherichia coli." J Bacteriol 192(20);5304-11. PMID: 20729367

Lal14: Lal PB, Schneider BL, Vu K, Reitzer L (2014). "The redundant aminotransferases in lysine and arginine synthesis and the extent of aminotransferase redundancy in Escherichia coli." Mol Microbiol 94(4);843-56. PMID: 25243376

Lam90: Lam HM, Winkler ME (1990). "Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12." J Bacteriol 1990;172(11);6518-28. PMID: 2121717

Lim94: Lim CJ, Hwang W, Park EH, Fuchs JA (1994). "Cyclic AMP-dependent expression of the Escherichia coli serC-aroA operon." Biochim Biophys Acta 1994;1218(2);250-3. PMID: 8018734

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Man97: Man TK, Pease AJ, Winkler ME (1997). "Maximization of transcription of the serC (pdxF)-aroA multifunctional operon by antagonistic effects of the cyclic AMP (cAMP) receptor protein-cAMP complex and Lrp global regulators of Escherichia coli K-12." J Bacteriol 1997;179(11);3458-69. PMID: 9171388

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Ravnikar87: Ravnikar PD, Somerville RL (1987). "Genetic characterization of a highly efficient alternate pathway of serine biosynthesis in Escherichia coli." J Bacteriol 169(6);2611-7. PMID: 3108237

Saito97: Saito K, Takagi Y, Ling HC, Takahashi H, Noji M (1997). "Molecular cloning, characterization and expression of cDNA encoding phosphoserine aminotransferase involved in phosphorylated pathway of serine biosynthesis from spinach." Plant Mol Biol 33(2);359-66. PMID: 9037153

Sakai02: Sakai A, Kita M, Katsuragi T, Tani Y (2002). "serC is involved in vitamin B6 biosynthesis in Escherichia coli but not in Bacillus subtilis." J Biosci Bioeng 93(3);334-7. PMID: 16233211

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wintermute10: Wintermute EH, Silver PA (2010). "Emergent cooperation in microbial metabolism." Mol Syst Biol 6;407. PMID: 20823845

Yoneyama11: Yoneyama H, Hori H, Lim SJ, Murata T, Ando T, Isogai E, Katsumata R (2011). "Isolation of a Mutant Auxotrophic for L-Alanine and Identification of Three Major Aminotransferases That Synthesize L-Alanine in Escherichia coli." Biosci Biotechnol Biochem 75(5);930-8. PMID: 21597182

Other References Related to Gene Regulation

Chung13: Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S (2013). "dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLoS Comput Biol 9(10);e1003246. PMID: 24146601


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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