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Escherichia coli K-12 substr. MG1655 Enzyme: phenylacetyl-CoA thioesterase



Gene: paaI Accession Numbers: G6717 (EcoCyc), b1396, ECK1393

Synonyms: ydbV

Regulation Summary Diagram: ?

Subunit composition of phenylacetyl-CoA thioesterase = [PaaI]4
         phenylacetyl-CoA thioesterase = PaaI

Summary:
PaaI belongs to the acyl-CoA thioesterase subfamily of the hotdog-fold superfamily of enzymes [Dillon04]. Among the relevant phenylacetate degradation pathway intermediates, its primary substrate appears to be phenylacetyl-CoA [Teufel12], although it was previously thought that its preferred substrates were ring-hydroxylated phenylacetyl-CoA thioesters [Song06b]. It may be involved in detoxification or salvage reactions for breakdown products of the unstable early intermediates of the phenylacetate degradation pathway [Teufel10, Teufel12].

A crystal structure of PaaI has been solved at 2 Å resolution [Song06b].

A paaI mutant does not exhibit a defect in utilization of phenylacetate as a source of carbon [Ismail03]. PaaI activity is increased in cells grown on phenylacetate [Teufel12].

PaaI: "phenylacetic acid degradation" [Ferrandez98]

Locations: cytosol

Map Position: [1,458,495 -> 1,458,917] (31.44 centisomes)
Length: 423 bp / 140 aa

Molecular Weight of Polypeptide: 14.851 kD (from nucleotide sequence), 14.7 kD (experimental) [Song06b ]

Molecular Weight of Multimer: 58 kD (experimental) [Song06b]

Unification Links: ASAP:ABE-0004666 , DIP:DIP-10428N , EchoBASE:EB3506 , EcoGene:EG13743 , EcoliWiki:b1396 , ModBase:P76084 , OU-Microarray:b1396 , PortEco:paaI , PR:PRO_000023479 , Protein Model Portal:P76084 , RefSeq:NP_415914 , RegulonDB:G6717 , SMR:P76084 , String:511145.b1396 , UniProt:P76084

Relationship Links: InterPro:IN-FAMILY:IPR003736 , InterPro:IN-FAMILY:IPR006683 , InterPro:IN-FAMILY:IPR011973 , PDB:Structure:1PSU , PDB:Structure:2FS2 , Pfam:IN-FAMILY:PF03061

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0016289 - CoA hydrolase activity Inferred from experiment [Song06b]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016790 - thiolester hydrolase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for paaI 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]

Credits:
Created 09-Feb-2006 by Keseler I , SRI International
Last-Curated ? 11-Jul-2014 by Keseler I , SRI International


Enzymatic reaction of: phenylacetyl-CoA thioesterase

phenylacetyl-CoA + H2O <=> phenylacetate + coenzyme A + H+

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.

Reversibility of this reaction is unspecified.

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
phenylacetyl-CoA
9.6
0.41
[Song06b]


Enzymatic reaction of: hydroxyphenylacetyl-CoA thioesterase

3,4-dihydroxyphenylacetyl-CoA + H2O <=> 3,4-dihydroxyphenylacetate + coenzyme A + H+

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.

Reversibility of this reaction is unspecified.

Alternative Substrates for 3,4-dihydroxyphenylacetyl-CoA: 4-hydroxyphenylacetyl-CoA [Song06b ] , 3-hydroxyphenylacetyl-CoA [Song06b ]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
3,4-dihydroxyphenylacetyl-CoA
16.0
100.0
[Song06b]
3-hydroxyphenylacetyl-CoA
21.0
86.0
[Song06b]
4-hydroxyphenylacetyl-CoA
35.0
79.0
[Song06b]

pH(opt): 6-9 [Song06b]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Song06b, UniProt11]
UniProt: Removed.
Chain 2 -> 140
[UniProt09]
UniProt: Acyl-coenzyme A thioesterase paaI;
Mutagenesis-Variant 46
[Song06b, UniProt11]
Alternate sequence: N → A; UniProt: Reduces activity 1000-fold.
Mutagenesis-Variant 52
[Song06b, UniProt11]
Alternate sequence: H → A; UniProt: Reduces activity 100-fold.
Mutagenesis-Variant 61
[Song06b, UniProt11]
Alternate sequence: D → A; UniProt: Loss of activity.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

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


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

Dillon04: Dillon SC, Bateman A (2004). "The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases." BMC Bioinformatics 5;109. PMID: 15307895

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

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

Song06b: Song F, Zhuang Z, Finci L, Dunaway-Mariano D, Kniewel R, Buglino JA, Solorzano V, Wu J, Lima CD (2006). "Structure, function and mechanism of the phenylacetate pathway hotdog-fold thioesterase PAAI." J Biol Chem 281(16);11028-38. PMID: 16464851

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

Teufel12: Teufel R, Friedrich T, Fuchs G (2012). "An oxygenase that forms and deoxygenates toxic epoxide." Nature 483(7389);359-62. PMID: 22398448

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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

Kim04d: 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


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, BIOCYC14B.