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Escherichia coli K-12 substr. MG1655 Enzyme: predicted 2,3-dehydroadipyl-CoA hydratase



Gene: paaF Accession Numbers: G6714 (EcoCyc), b1393, ECK1390

Synonyms: ydbR, ydbS

Regulation Summary Diagram: ?

Component of: PaaF-PaaG hydratase-isomerase complex (summary available)

Summary:
PaaF is a predicted 2,3-dehydroadipyl-CoA hydratase involved in phenylacetate catabolism. The enzyme from Pseudomonas sp. strain Y2 has been biochemically characterized [Teufel10].

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

PaaF: "phenylacetic acid degradation" [Ferrandez98]

Citations: [Park04a]

Locations: inner membrane

Map Position: [1,455,521 -> 1,456,288] (31.37 centisomes)
Length: 768 bp / 255 aa

Molecular Weight of Polypeptide: 27.237 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004659 , DIP:DIP-10425N , EchoBASE:EB3503 , EcoGene:EG13740 , EcoliWiki:b1393 , ModBase:P76082 , OU-Microarray:b1393 , PortEco:paaF , Pride:P76082 , Protein Model Portal:P76082 , RefSeq:NP_415911 , RegulonDB:G6714 , SMR:P76082 , String:511145.b1393 , Swiss-Model:P76082 , UniProt:P76082

Relationship Links: InterPro:IN-FAMILY:IPR001753 , InterPro:IN-FAMILY:IPR018376 , PDB:Structure:4FZW , Pfam:IN-FAMILY:PF00378 , Prosite:IN-FAMILY:PS00166

In Paralogous Gene Group: 12 (7 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ismail03]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006631 - fatty acid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004300 - enoyl-CoA hydratase activity Inferred from experiment Inferred by computational analysis [GOA01, Teufel10]
GO:0005515 - protein binding Inferred from experiment [Grishin12]
GO:0042802 - identical protein binding Inferred from experiment [Grishin12]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for paaF 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:
Last-Curated ? 26-Oct-2012 by Keseler I , SRI International


Enzymatic reaction of: 2,3-dehydroadipyl-CoA hydratase

3-hydroxyadipyl-CoA <=> 2,3-didehydroadipyl-CoA + H2O

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 phenylethylamine degradation , phenylacetate degradation I (aerobic)


Subunit of: PaaF-PaaG hydratase-isomerase complex

Subunit composition of PaaF-PaaG hydratase-isomerase complex = [PaaG]6[PaaF]6
         predicted ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming) = PaaG (summary available)
         predicted 2,3-dehydroadipyl-CoA hydratase = PaaF (summary available)

Summary:
A crystal structure of the PaaF-PaaG complex shows two homotrimeric discs of PaaF subunits that pack head-to-head, sandwiched by two homotrimeric discs of PaaG subunits. The center of the disks forms an open channel with a diameter of 9 Å [Grishin12].

Credits:
Created 19-Oct-2012 by Keseler I , SRI International
Last-Curated ? 19-Oct-2012 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 11
[UniProt10a]
Alternate sequence: R → Q; UniProt: (in strain: W);
Extrinsic-Sequence-Variant 32
[UniProt10a]
Alternate sequence: M → T; UniProt: (in strain: W);
Extrinsic-Sequence-Variant 45
[UniProt10a]
Alternate sequence: T → S; UniProt: (in strain: W);


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

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."

Grishin12: Grishin AM, Ajamian E, Zhang L, Rouiller I, Bostina M, Cygler M (2012). "Protein-Protein Interactions in the β-Oxidation Part of the Phenylacetate Utilization Pathway. Crystal Structure of the PaaF-PaaG Hydratase-Isomerase Complex." J Biol Chem. PMID: 22961985

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

Park04a: Park SJ, Yup Lee S (2004). "New FadB homologous enzymes and their use in enhanced biosynthesis of medium-chain-length polyhydroxyalkanoates in FadB mutant Escherichia coli." Biotechnol Bioeng 86(6);681-6. PMID: 15137080

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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

Kim04c: 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 Sat Dec 20, 2014, BIOCYC13B.