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Escherichia coli K-12 substr. MG1655 Enzyme: L-serine deaminase III



Gene: tdcG Accession Numbers: G7624 (EcoCyc), b4471, ECK3101

Synonyms: b3111 (obsolete), yhaQ, b3112 (obsolete), tdcGa, yhaP, sdhY, L-serine dehydratase 3

Regulation Summary Diagram: ?

Subunit composition of L-serine deaminase III = [TdcG]2
         L-serine deaminase III = TdcG

Summary:
L-serine deaminase III (TdcG) is one of three enzymes carrying out the sole step in the pathway of L-serine degradation, converting serine into a basic cellular building block, pyruvate.

TdcG catalyzes the conversion of L-serine into pyruvate and ammonia [Burman04].

Like the other two known serine deaminases, TdcG has a catalytically critical iron-sulfur cluster that is destroyed by exposure to oxygen [Burman04].

tdcG is part of an operon that is induced under anaerobic conditions [Hesslinger98]. A notable member of this operon is the catabolic threonine deaminase gene tdcB. The presence of both genes on the same operon likely explains early observations that suggested the existence of a bifunctional threonine/serine deaminase [Umbarger57]. Expression of tdcG is also limited by glucose, much like fellow serine deaminase gene sdaB [Sawers01].

Gene Citations: [Hagewood94]

Map Position: [3,256,307 <- 3,257,671] (70.18 centisomes)
Length: 1365 bp / 454 aa

Molecular Weight of Polypeptide: 48.522 kD (from nucleotide sequence), 46.0 kD (experimental) [Burman04 ]

Isozyme Sequence Similarity:
L-serine deaminase I: YES ,
L-serine deaminase II: YES

Unification Links: ASAP:ABE-0174101 , DIP:DIP-10974N , EchoBASE:EB2610 , EcoGene:EG12756 , EcoliWiki:b4471 , OU-Microarray:b3112 , PortEco:tdcG , PR:PRO_000024043 , Protein Model Portal:P42630 , RefSeq:YP_026204 , RegulonDB:G7624 , SMR:P42630 , String:511145.b4471 , UniProt:P42630

Relationship Links: InterPro:IN-FAMILY:IPR004644 , InterPro:IN-FAMILY:IPR005130 , InterPro:IN-FAMILY:IPR005131 , Pfam:IN-FAMILY:PF03313 , Pfam:IN-FAMILY:PF03315

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009063 - cellular amino acid catabolic process Inferred from experiment [Burman04]
GO:0006094 - gluconeogenesis Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0070689 - L-threonine catabolic process to propionate Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0003941 - L-serine ammonia-lyase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Burman04]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]

MultiFun Terms: metabolism carbon utilization amino acids

Essentiality data for tdcG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Credits:
Created 18-Sep-2007 by Shearer A , SRI International


Enzymatic reaction of: serine deaminase

L-serine <=> 2-aminoprop-2-enoate + H+ + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: L-serine degradation

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Burman04]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-serine
420000.0
[Newman80b, BRENDA14]
L-serine
2670.0
436.0
[Cicchillo04, BRENDA14]
L-serine
4800.0
544.0
[Burman04, BRENDA14]

T(opt): 37 °C [BRENDA14, Anfora07]


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/21/2004 (paley) Merged genes G7624-2/tdcG_2 into G7624/tdcG_1
12/8/1998 (pkarp) Merged genes G7625/b3112 and G7624/b3111 Hesslinger et al have determined that these two ORFs are in fact a single gene, due to a sequencing error [Hesslinger98b ][Hesslinger98b]
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Anfora07: Anfora AT, Haugen BJ, Roesch P, Redford P, Welch RA (2007). "Roles of serine accumulation and catabolism in the colonization of the murine urinary tract by Escherichia coli CFT073." Infect Immun 75(11);5298-304. PMID: 17785472

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Burman04: Burman JD, Harris RL, Hauton KA, Lawson DM, Sawers RG (2004). "The iron-sulfur cluster in the L-serine dehydratase TdcG from Escherichia coli is required for enzyme activity." FEBS Lett 576(3);442-4. PMID: 15498577

Cicchillo04: Cicchillo RM, Baker MA, Schnitzer EJ, Newman EB, Krebs C, Booker SJ (2004). "Escherichia coli L-serine deaminase requires a [4Fe-4S] cluster in catalysis." J Biol Chem 279(31);32418-25. PMID: 15155761

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Hagewood94: Hagewood BT, Ganduri YL, Datta P (1994). "Functional analysis of the tdcABC promoter of Escherichia coli: roles of TdcA and TdcR." J Bacteriol 1994;176(20);6214-20. PMID: 7928991

Hesslinger98: Hesslinger C, Fairhurst SA, Sawers G (1998). "Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate." Mol Microbiol 1998;27(2);477-92. PMID: 9484901

Hesslinger98b: Hesslinger C, Fairhurst SA, Sawers G "Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate." Molecular Microbiology 27:477-492, 1998.

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

Newman80b: Newman EB, Kapoor V (1980). "In vitro studies on L-serine deaminase activity of Escherichia coli K12." Can J Biochem 1980;58(11);1292-7. PMID: 7011505

Sawers01: Sawers G (2001). "A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon." Mol Microbiol 39(5);1285-98. PMID: 11251844

Umbarger57: Umbarger HE, Brown B (1957). "Threonine deamination in Escherichia coli. II. Evidence for two L-threonine deaminases." J Bacteriol 73(1);105-12. PMID: 13405870

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Kim11c: Kim M, Lim S, Ryu S (2011). "Comparison of tdcA Expression Between Escherichia coli and Salmonella enterica Serovar Typhimurium." J Microbiol Biotechnol 21(3);252-5. PMID: 21464594

Wu92: Wu Y, Patil RV, Datta P (1992). "Catabolite gene activator protein and integration host factor act in concert to regulate tdc operon expression in Escherichia coli." J Bacteriol 1992;174(21);6918-27. PMID: 1328166

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


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 Fri Nov 28, 2014, biocyc13.