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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
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MetaCyc Enzyme: ring 1,2-phenylacetyl-CoA epoxidase

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of ring 1,2-phenylacetyl-CoA epoxidase = [PaaE][PaaA][PaaC][PaaB]
         ring 1,2-phenylacetyl-CoA epoxidase, reductase subunit = PaaE (summary available)
         ring 1,2-phenylacetyl-CoA epoxidase, monooxygenase subunit = PaaA (summary available)
         ring 1,2-phenylacetyl-CoA epoxidase, structural subunit = PaaC (summary available)
         ring 1,2-phenylacetyl-CoA epoxidase subunit = PaaB (summary available)

Summary:
The ring 1,2-phenylacetyl-CoA epoxidase, comprised of the PaaA, PaaB, PaaC, and PaaE polypeptides, catalyzes the second step in the aerobic degradation of phenylacetate [Grishin11].

Stable subcomplexes composed of PaaABC, PaaAC and PaaBC can be purified, but only the combination of the PaaABC complex together with PaaE has full activity [Grishin11]. Crystal structures of the PaaAC subcomplex alone and together with a variety of ligands have been solved [Grishin10, Grishin11].

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment [Grishin11]
Molecular Function: GO:0016709 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen Inferred from experiment [Grishin11]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: ring 1,2-phenylacetyl-CoA epoxidase

Synonyms: phenylacetyl-CoA monooxygenase

EC Number: 1.14.13.149

phenylacetyl-CoA + NADPH + oxygen + H+ <=> 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + NADP+ + 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.

The reaction is physiologically favored in the direction shown.

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: [2Fe-2S] iron-sulfur cluster [Grishin11], FAD [Grishin11]


Subunit of ring 1,2-phenylacetyl-CoA epoxidase: ring 1,2-phenylacetyl-CoA epoxidase, reductase subunit

Synonyms: YdbR, PaaE

Gene: paaE Accession Numbers: G6713 (MetaCyc), b1392, ECK1389

Locations: cytosol

Sequence Length: 356 AAs

Molecular Weight: 39.32 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01, Ferrandez98]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0050660 - flavin adenine dinucleotide binding Inferred from experiment [Grishin11]
GO:0051537 - 2 iron, 2 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Grishin11]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Unification Links: EcoliWiki:b1392 , ModBase:P76081 , Protein Model Portal:P76081 , RefSeq:NP_415910 , SMR:P76081 , String:511145.b1392 , Swiss-Model:P76081 , UniProt:P76081

Relationship Links: InterPro:IN-FAMILY:IPR001041 , InterPro:IN-FAMILY:IPR001221 , InterPro:IN-FAMILY:IPR001433 , InterPro:IN-FAMILY:IPR001709 , InterPro:IN-FAMILY:IPR006058 , InterPro:IN-FAMILY:IPR008333 , InterPro:IN-FAMILY:IPR011884 , InterPro:IN-FAMILY:IPR012675 , InterPro:IN-FAMILY:IPR017927 , InterPro:IN-FAMILY:IPR017938 , Pfam:IN-FAMILY:PF00111 , Pfam:IN-FAMILY:PF00175 , Pfam:IN-FAMILY:PF00970 , Prints:IN-FAMILY:PR00371 , Prints:IN-FAMILY:PR00410 , Prosite:IN-FAMILY:PS00197 , Prosite:IN-FAMILY:PS51085 , Prosite:IN-FAMILY:PS51384

Summary:
PaaE has similarity to class IA-like reductases, members of the ferredoxin-NADP+ reductase (FNR) family of proteins [Ferrandez98]. PaaE carries a [2Fe-2S] cluster similar to that of spinach ferredoxin [Grishin11].

PaaE: "phenylacetic acid degradation" [Ferrandez98]


Subunit of ring 1,2-phenylacetyl-CoA epoxidase: ring 1,2-phenylacetyl-CoA epoxidase, monooxygenase subunit

Synonyms: YdbO, PaaA

Gene: paaA Accession Numbers: G6709 (MetaCyc), b1388, ECK1385

Locations: cytosol

Sequence Length: 309 AAs

Molecular Weight: 35.499 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ferrandez98]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0097266 - phenylacetyl-CoA 1,2-epoxidase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Unification Links: EcoliWiki:b1388 , ModBase:P76077 , PR:PRO_000023475 , Pride:P76077 , Protein Model Portal:P76077 , RefSeq:NP_415906 , SMR:P76077 , String:511145.b1388 , UniProt:P76077

Relationship Links: InterPro:IN-FAMILY:IPR007814 , InterPro:IN-FAMILY:IPR009078 , InterPro:IN-FAMILY:IPR011881 , InterPro:IN-FAMILY:IPR012347 , PDB:Structure:3PVR , PDB:Structure:3PVT , PDB:Structure:3PVY , PDB:Structure:3PW1 , PDB:Structure:3PW8 , PDB:Structure:3PWQ , Pfam:IN-FAMILY:PF05138

Summary:
PaaA is the catalytic α subunit of the catalytic core of the enzyme [Grishin11]. PaaA has similarity to the large (α) subunit of diiron monooxygenase complexes [Ferrandez98].

PaaA: "phenylacetic acid degradation" [Ferrandez98]


Subunit of ring 1,2-phenylacetyl-CoA epoxidase: ring 1,2-phenylacetyl-CoA epoxidase, structural subunit

Synonyms: YdbP, PaaC

Gene: paaC Accession Numbers: G6711 (MetaCyc), b1390, ECK1387

Locations: cytosol

Sequence Length: 248 AAs

Molecular Weight: 27.877 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ferrandez98]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]

MultiFun Terms: metabolism carbon utilization carbon compounds

Unification Links: EcoliWiki:b1390 , ModBase:P76079 , PR:PRO_000023477 , Pride:P76079 , Protein Model Portal:P76079 , RefSeq:NP_415908 , SMR:P76079 , String:511145.b1390 , UniProt:P76079

Relationship Links: InterPro:IN-FAMILY:IPR007814 , InterPro:IN-FAMILY:IPR009078 , InterPro:IN-FAMILY:IPR011882 , InterPro:IN-FAMILY:IPR012347 , PDB:Structure:1OTK , PDB:Structure:3PVR , PDB:Structure:3PVT , PDB:Structure:3PVY , PDB:Structure:3PW1 , PDB:Structure:3PW8 , PDB:Structure:3PWQ , Pfam:IN-FAMILY:PF05138

Summary:
PaaC is the structural β subunit of the catalytic core of the enzyme [Grishin11].

PaaC: "phenylacetic acid degradation" [Ferrandez98]


Subunit of ring 1,2-phenylacetyl-CoA epoxidase: ring 1,2-phenylacetyl-CoA epoxidase subunit

Synonyms: YnbF, PaaB

Gene: paaB Accession Numbers: G6710 (MetaCyc), b1389, ECK1386

Sequence Length: 95 AAs

Molecular Weight: 10.942 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0010124 - phenylacetate catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Ferrandez98]

MultiFun Terms: metabolism carbon utilization carbon compounds

Unification Links: EcoliWiki:b1389 , PR:PRO_000023476 , Protein Model Portal:P76078 , RefSeq:NP_415907 , SMR:P76078 , String:511145.b1389 , UniProt:P76078

Relationship Links: InterPro:IN-FAMILY:IPR009359 , Pfam:IN-FAMILY:PF06243

Summary:
PaaB has similarity to the activator protein of diiron monooxygenase complexes [Ferrandez98].

PaaB: "phenylacetic acid degradation" [Ferrandez98]


References

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

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.

Grishin10: Grishin AM, Ajamian E, Zhang L, Cygler M (2010). "Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complex." Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 9);1045-9. PMID: 20823522

Grishin11: Grishin AM, Ajamian E, Tao L, Zhang L, Menard R, Cygler M (2011). "Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex." J Biol Chem 286(12);10735-43. PMID: 21247899

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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

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."

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, BIOCYC13B.