Escherichia coli K-12 substr. MG1655 Enzyme: β-ketoadipyl-CoA thiolase

Gene: paaJ Accession Numbers: G6718 (EcoCyc), b1397, ECK1394

Synonyms: ydbW

Regulation Summary Diagram: ?

Regulation summary diagram for paaJ

PaaJ is a β-ketoadipyl-CoA thiolase catalyzing two steps in phenylacetate catabolism [Ismail03, Nogales07, Teufel10].

A paaJ mutant exhibits a defect in utilization of phenylacetate as a source of carbon [Ismail03].

PaaJ: "phenylacetic acid degradation" [Ferrandez98]

Review, including new consensus gene names: [Luengo01]

Locations: cytosol

Map Position: [1,458,917 -> 1,460,122] (31.44 centisomes, 113°)
Length: 1206 bp / 401 aa

Molecular Weight of Polypeptide: 42.277 kD (from nucleotide sequence), 43 kD (experimental) [Nogales07 ]

Unification Links: ASAP:ABE-0004668 , EchoBASE:EB3507 , EcoGene:EG13744 , EcoliWiki:b1397 , ModBase:P77525 , OU-Microarray:b1397 , PortEco:paaJ , Pride:P0C7L2 , Protein Model Portal:P0C7L2 , RefSeq:NP_415915 , RegulonDB:G6718 , SMR:P0C7L2 , String:511145.b1397 , Swiss-Model:P77525 , UniProt:P0C7L2

Relationship Links: InterPro:IN-FAMILY:IPR002155 , InterPro:IN-FAMILY:IPR012793 , InterPro:IN-FAMILY:IPR016038 , InterPro:IN-FAMILY:IPR016039 , InterPro:IN-FAMILY:IPR020610 , InterPro:IN-FAMILY:IPR020613 , InterPro:IN-FAMILY:IPR020615 , InterPro:IN-FAMILY:IPR020616 , InterPro:IN-FAMILY:IPR020617 , Panther:IN-FAMILY:PTHR18919 , Pfam:IN-FAMILY:PF00108 , Pfam:IN-FAMILY:PF02803 , Prosite:IN-FAMILY:PS00098 , Prosite:IN-FAMILY:PS00099 , Prosite:IN-FAMILY:PS00737

In Paralogous Gene Group: 286 (5 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for paaJ

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ferrandez98, Ismail03]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0019619 - protocatechuate catabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016740 - transferase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Nogales07]
GO:0033812 - 3-oxoadipyl-CoA thiolase activity Inferred from experiment Inferred by computational analysis [GOA01, Nogales07]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11a]
GO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for paaJ 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]

Last-Curated ? 06-Aug-2010 by Keseler I , SRI International

Enzymatic reaction of: 3-oxo-5,6-dehydrosuberyl-CoA thiolase (β-ketoadipyl-CoA thiolase)

EC Number:

2,3-didehydroadipyl-CoA + acetyl-CoA <=> 3-oxo-5,6-didehydrosuberyl-CoA + coenzyme A

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

The reaction is favored in the opposite direction.

In Pathways: superpathway of phenylethylamine degradation , phenylacetate degradation I (aerobic)

Enzymatic reaction of: β-ketoadipyl-CoA thiolase

EC Number:

3-oxoadipyl-CoA + coenzyme A <=> succinyl-CoA + acetyl-CoA

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

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of phenylethylamine degradation , phenylacetate degradation I (aerobic)

Sequence Features

Protein sequence of beta-ketoadipyl-CoA thiolase with features indicated

Feature Class Location Citations Comment
Active-Site 90
UniProt: Acyl-thioester intermediate; Non-Experimental Qualifier: by similarity;
Active-Site 357
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Active-Site 387
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Ferrandez98: Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E (1998). "Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway." J Biol Chem 1998;273(40);25974-86. PMID: 9748275

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."

Ismail03: Ismail W, El-Said Mohamed M, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher A, Fuchs G (2003). "Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli." Eur J Biochem 270(14);3047-54. PMID: 12846838

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Luengo01: Luengo JM, Garcia JL, Olivera ER (2001). "The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications." Mol Microbiol 39(6);1434-42. PMID: 11260461

Nogales07: Nogales J, Macchi R, Franchi F, Barzaghi D, Fernandez C, Garcia JL, Bertoni G, Diaz E (2007). "Characterization of the last step of the aerobic phenylacetic acid degradation pathway." Microbiology 153(Pt 2);357-65. PMID: 17259607

Teufel10: Teufel R, Mascaraque V, Ismail W, Voss M, Perera J, Eisenreich W, Haehnel W, Fuchs G (2010). "Bacterial phenylalanine and phenylacetate catabolic pathway revealed." Proc Natl Acad Sci U S A 107(32):14390-5. PMID: 20660314

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11a: 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

Beisel12: Beisel CL, Updegrove TB, Janson BJ, Storz G (2012). "Multiple factors dictate target selection by Hfq-binding small RNAs." EMBO J 31(8);1961-74. PMID: 22388518

Ferrandez00: Ferrandez A, Garcia JL, Diaz E (2000). "Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli." J Biol Chem 275(16);12214-22. PMID: 10766858

Kim04b: Kim HS, Kang TS, Hyun JS, Kang HS (2004). "Regulation of penicillin G acylase gene expression in Escherichia coli by repressor PaaX and the cAMP-cAMP receptor protein complex." J Biol Chem 279(32);33253-62. PMID: 15159386

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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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