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Escherichia coli K-12 substr. MG1655 Enzyme: propionate kinase



Gene: tdcD Accession Numbers: EG11172 (EcoCyc), b3115, ECK3104

Synonyms: yhaA

Regulation Summary Diagram: ?

Summary:
The tdcD gene encodes a protein with propionate and acetate kinase activity. Propionate kinase functions in the anaerobic degradation of threonine [Hesslinger98].

Evidence suggests that TdcD also catalyzes the reverse reaction converting propionyl-phosphate and ADP to propionate and ATP, which is the last step in pathway threonine degradation I. E. coli double null mutants deficient in TdcD and AckA activity, or Pta and AckA activity were unable to metabolize threonine to propionate. This suggested the occurrence of both this reaction and the preceding reaction that converts propanoyl-CoA and phosphate to propionyl-phosphate and coenzyme A in this pathway [Hesslinger98].

Based on sequence similarity, TdcD was predicted to be an acetate kinase [Reed03].

Overexpression of tdcD partially rescues the anaerobic growth defect of an ackA mutant. A tdcD deletion mutant has no obvious phenotype [Hesslinger98].

E. coli TdcD shows 42% identity and 62% overall similarity with TdcD from Salmonella enterica subsp. enterica serovar Typhimurium. The crystal structure of TdcD from Salmonella enterica subsp. enterica serovar Typhimurium has been determined and kinetic studies showed that the enzyme had approximately tenfold higher affinity for propionate than for acetate [Simanshu05, Simanshu05a, Simanshu08].

Review: [Simanshu07]

Gene Citations: [Hagewood94, Sawers01]

Locations: cytosol

Map Position: [3,260,474 <- 3,261,694] (70.27 centisomes)
Length: 1221 bp / 406 aa

Molecular Weight of Polypeptide: 43.929 kD (from nucleotide sequence)

Isozyme Sequence Similarity:
acetate kinase: YES

Unification Links: ASAP:ABE-0010245 , DIP:DIP-10971N , EchoBASE:EB1159 , EcoGene:EG11172 , EcoliWiki:b3115 , Mint:MINT-1273849 , ModBase:P11868 , OU-Microarray:b3115 , PortEco:tdcD , PR:PRO_000024040 , Protein Model Portal:P11868 , RefSeq:NP_417585 , RegulonDB:EG11172 , SMR:P11868 , String:511145.b3115 , Swiss-Model:P11868 , UniProt:P11868

Relationship Links: InterPro:IN-FAMILY:IPR000890 , InterPro:IN-FAMILY:IPR004372 , InterPro:IN-FAMILY:IPR023865 , InterPro:IN-FAMILY:IPR024917 , Panther:IN-FAMILY:PTHR21060 , Panther:IN-FAMILY:PTHR21060:SF9 , Pfam:IN-FAMILY:PF00871 , Prints:IN-FAMILY:PR00471 , Prosite:IN-FAMILY:PS01075 , Prosite:IN-FAMILY:PS01076

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006567 - threonine catabolic process Inferred from experiment [Hesslinger98]
GO:0019665 - anaerobic amino acid catabolic process Inferred from experiment [Hesslinger98]
GO:0006082 - organic acid metabolic process Inferred by computational analysis [GOA01]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0070689 - L-threonine catabolic process to propionate Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0008776 - acetate kinase activity Inferred from experiment [Hesslinger98]
GO:0008980 - propionate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Hesslinger98]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016774 - phosphotransferase activity, carboxyl group as acceptor Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism threonine catabolism

Essentiality data for tdcD 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 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Curated 27-Nov-2007 by Keseler I , SRI International
Last-Curated ? 10-Nov-2011 by Fulcher C , SRI International


Enzymatic reaction of: propionate kinase

Synonyms: propanoate kinase

EC Number: 2.7.2.15

ATP + propanoate <=> ADP + propanoyl phosphate

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. [Hesslinger98]

Alternative Substrates for propanoate: acetate [Hesslinger98 ]

In Pathways: superpathway of threonine metabolism , threonine degradation I

Summary:
Recombinantly overexpressed TdcD was shown to have both propionate kinase and acetate kinase activity, with propionate kinase activity being marginally higher [Hesslinger98].


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 11
[UniProt13]
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 11
[UniProt12]
UniProt: ADP; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 18
[UniProt13]
UniProt: ATP; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 86
[UniProt13]
UniProt: Substrate; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 121
[Goss88, Schweizer89, UniProt10]
Alternate sequence: L → P; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Sequence-Conflict 141
[Goss88, Schweizer89, UniProt10]
Alternate sequence: T → L; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Active-Site 143
[UniProt13]
UniProt: Proton donor/acceptor; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 175
[UniProt12]
UniProt: ADP; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 198
[Goss88, Schweizer89, UniProt10]
Alternate sequence: E → A; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Amino-Acid-Site 236
[UniProt13]
UniProt: Transition state stabilizer; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Sequence-Conflict 244
[Goss88, Schweizer89, UniProt10]
Alternate sequence: V → P; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Sequence-Conflict 249 -> 250
[Goss88, Schweizer89, UniProt10]
Alternate sequence: MS → RR; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Sequence-Conflict 275
[Goss88, Schweizer89, UniProt10]
Alternate sequence: G → H; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);
Sequence-Conflict 283
[Goss88, Schweizer89, UniProt10]
Alternate sequence: L → G; UniProt: (in Ref. 3; CAA32595 and 4; AAA24663);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3115 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11172; 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

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

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, 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.

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

Goss88: Goss TJ, Schweizer HP, Datta P (1988). "Molecular characterization of the tdc operon of Escherichia coli K-12." J Bacteriol 1988;170(11);5352-9. PMID: 3053659

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

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

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

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

Schweizer89: Schweizer HP, Datta P (1989). "The complete nucleotide sequence of the tdc region of Escherichia coli." Nucleic Acids Res 1989;17(10);3994. PMID: 2660107

Simanshu05: Simanshu DK, Savithri HS, Murthy MR (2005). "Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily." J Mol Biol 352(4);876-92. PMID: 16139298

Simanshu05a: Simanshu DK, Murthy MR (2005). "Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium." Acta Crystallogr Sect F Struct Biol Cryst Commun 61(Pt 1);52-5. PMID: 16508089

Simanshu07: Simanshu DK, Chittori S, Savithri HS, Murthy MR (2007). "Structure and function of enzymes involved in the anaerobic degradation of L-threonine to propionate." J Biosci 32(6);1195-206. PMID: 17954980

Simanshu08: Simanshu DK, Savithri HS, Murthy MR (2008). "Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity." Proteins 70(4);1379-88. PMID: 17894350

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

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

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

Kim11b: 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

Wu92c: 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 Mon Dec 22, 2014, biocyc13.