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KEGG pathways | MAP code | Pathways |
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MAP00624 | 1- and 2-Methylnaphthalene degradation | MAP00626 | Naphthalene and anthracene degradation | MAP00628 | Fluorene degradation | MAP00642 | Ethylbenzene degradation |
UniProtKB:Accession Number | P0A110 | P0A111 | P0A112 | P0A113 |
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Entry name | NDOB_PSEPU | NDOB_PSEU8 | NDOC_PSEPU | NDOC_PSEU8 |
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Activity | Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+). | Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+). | Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+). | Naphthalene + NADH + O(2) = (1R,2S)-1,2- dihydronaphthalene-1,2-diol + NAD(+). |
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Subunit | Naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase (ndoR) and ferredoxin (ndoA), and ISP is composed of a large alpha subunit (ndoB) and a small beta subunit (ndoC). | Naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase and ferredoxin (doxA), and ISP is composed of a large alpha subunit (doxB) and a small beta subunit (doxD) (Probable). | The naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase (ndoR) and ferredoxin (ndoA), and ISP is composed of a hexamer of three large alpha subunits (ndoB) and three small beta subunits (ndoC). | Naphthalene dioxygenase (NDO) multicomponent enzyme system is composed of an electron transfer component and an iron sulfur protein (ISP). The electron transfer component is composed of ferredoxin reductase and ferredoxin (doxA), and ISP is composed of a large alpha subunit (doxB) and a small beta subunit (doxD) (Probable). |
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Subcellular location |
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Cofactor | Binds 1 2Fe-2S cluster (Probable).,Binds 1 iron ion (Probable). | Binds 1 2Fe-2S cluster (By similarity).,Binds 1 iron ion (By similarity). | Binds 1 2Fe-2S cluster (Probable).,Binds 1 iron ion (Probable). | Binds 1 2Fe-2S cluster (By similarity).,Binds 1 iron ion (By similarity). |
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Compound table: links to PDB-related databases & PoSSuM |
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| Cofactors | Substrates | Products |
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KEGG-id | L00023 | C00023 | C00829 | C00004 | C00007 | C00080 | C04314 | C00003 |
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Compound | [2Fe-2S] | Iron | Naphthalene | NADH | O2 | H+ | (1R,2S)-1,2-dihydronaphthalene-1,2-diol | NAD+ |
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Type | heavy metal,sulfide group | heavy metal | aromatic ring (only carbon atom) | amide group,amine group,nucleotide | others | others | aromatic ring (only carbon atom),carbohydrate | amide group,amine group,nucleotide |
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ChEBI | 33739
| 18248 82664
| 16482
| 16908
| 15379 26689 27140
| 15378
| 44343
| 15846
|
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PubChem |
| 23925
| 931
| 439153
| 977
| 1038
| 440294
| 5893
|
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| | | | | | | | | | | | | | | |
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1eg9A01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Analogue:IND | Unbound | Unbound | | Unbound | Unbound |
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1ndoA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoC01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoE01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7gA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Bound:NPY | Unbound | Unbound | | Unbound | Unbound |
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1o7hA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7mA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Bound:OXY | | Unbound | Unbound |
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1o7nA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Analogue:IND | Unbound | Bound:OXY | | Unbound | Unbound |
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1o7pA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Bound:NDH | Unbound |
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1o7wA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1uuvA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Analogue:IND | Unbound | Analogue:_NO | | Unbound | Unbound |
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1uuwA01 |  |  |  |  |  |  |  | Unbound | Bound:_FE | Unbound | Unbound | Analogue:_NO | | Unbound | Unbound |
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1eg9A02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoC02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoE02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7gA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7hA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7mA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7nA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7pA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7wA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1uuvA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1uuwA02 |  |  |  |  |  |  |  | Bound:FES | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1eg9B |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoD |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1ndoF |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7gB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7hB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7mB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7nB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7pB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1o7wB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1uuvB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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1uuwB |  |  |  |  |  |  |  | Unbound | Unbound | Unbound | Unbound | Unbound | | Unbound | Unbound |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[3] | SCHEME I, p.30257-30260 |
| [4] | p.575-582 |
| [5] | p.11068-11070 |
| [7] | Fig.1, p.1835-1836 |
| [9] | Fig.2 |
| [11] | Scheme 1, p.706-709 |
| [14] | Scheme 2, p.1952 |
| [17] | Fig.1, P.7065-7066 |
| [18] | p.272-274 |
| [19] | Fig.2 |
| [20] | Fig |
| [21] | Scheme 2, Scheme 3, Fig.7, Fig.9, p.443-451 |
| [22] |
|
|
references | [1] |
---|
PubMed ID | 7858982 |
---|
Journal | Bioorg Med Chem |
---|
Year | 1994 |
---|
Volume | 2 |
---|
Pages | 727-34 |
---|
Authors | Whited GM, Downie JC, Hudlicky T, Fearnley SP, Dudding TC, Olivo HF, Parker D |
---|
Title | Oxidation of 2-methoxynaphthalene by toluene, naphthalene and biphenyl dioxygenases:structure and absolute stereochemistry of metabolites. |
---|
[2] |
---|
PubMed ID | 8899998 |
---|
Journal | Appl Environ Microbiol |
---|
Year | 1996 |
---|
Volume | 62 |
---|
Pages | 4073-80 |
---|
Authors | Resnick SM, Gibson DT |
---|
Title | Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. |
---|
[3] |
---|
PubMed ID | 9374510 |
---|
Journal | J Biol Chem |
---|
Year | 1997 |
---|
Volume | 272 |
---|
Pages | 30254-60 |
---|
Authors | Di Gennaro P, Sello G, Bianchi D, D'Amico P |
---|
Title | Specificity of substrate recognition by Pseudomonas fluorescens N3 dioxygenase. The role of the oxidation potential and molecular geometry. |
---|
[4] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) |
---|
Medline ID | 98298434 |
---|
PubMed ID | 9634695 |
---|
Journal | Structure |
---|
Year | 1998 |
---|
Volume | 6 |
---|
Pages | 571-86 |
---|
Authors | Kauppi B, Lee K, Carredano E, Parales RE, Gibson DT, Eklund H, Ramaswamy S |
---|
Title | Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. |
---|
Related PDB | 1ndo |
---|
Related UniProtKB | P0A110,P0A111,P23094,P23095 |
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[5] |
---|
PubMed ID | 10390817 |
---|
Journal | Appl Microbiol Biotechnol |
---|
Year | 1999 |
---|
Volume | 51 |
---|
Pages | 592-7 |
---|
Authors | Barriault D, Sylvestre M |
---|
Title | Functionality of biphenyl 2,3-dioxygenase components in naphthalene 1,2-dioxygenase. |
---|
[6] |
---|
PubMed ID | 10460161 |
---|
Journal | Biochemistry |
---|
Year | 1999 |
---|
Volume | 38 |
---|
Pages | 11062-72 |
---|
Authors | Coulter ED, Moon N, Batie CJ, Dunham WR, Ballou DP |
---|
Title | Electron paramagnetic resonance measurements of the ferrous mononuclear site of phthalate dioxygenase substituted with alternate divalent metal ions: direct evidence for ligation of two histidines in the copper(II)-reconstituted protein. |
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[7] |
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PubMed ID | 10074076 |
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Journal | J Bacteriol |
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Year | 1999 |
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Volume | 181 |
---|
Pages | 1831-7 |
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Authors | Parales RE, Parales JV, Gibson DT |
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Title | Aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity. |
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[8] |
---|
PubMed ID | 10713518 |
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Journal | Acta Crystallogr D Biol Crystallogr |
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Year | 2000 |
---|
Volume | 56 |
---|
Pages | 313-21 |
---|
Authors | Carredano E, Kauppi B, Choudhury D, Ramaswamy S |
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Title | Pseudo-symmetry characterization and refinement of a trigonal crystal form of naphthalene 1,2-dioxygenase. |
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[9] |
---|
PubMed ID | 10692370 |
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Journal | J Bacteriol |
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Year | 2000 |
---|
Volume | 182 |
---|
Pages | 1641-9 |
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Authors | Parales RE, Lee K, Resnick SM, Jiang H, Lessner DJ, Gibson DT |
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Title | Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. |
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[10] |
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PubMed ID | 10986254 |
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Journal | J Bacteriol |
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Year | 2000 |
---|
Volume | 182 |
---|
Pages | 5495-504 |
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Authors | Parales RE, Resnick SM, Yu CL, Boyd DR, Sharma ND, Gibson DT |
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Title | Regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit. |
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[11] |
---|
Comments | X-ray crystallography |
---|
PubMed ID | 10669618 |
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Journal | J Mol Biol |
---|
Year | 2000 |
---|
Volume | 296 |
---|
Pages | 701-12 |
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Authors | Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S |
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Title | Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding. |
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Related PDB | 1eg9 |
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[12] |
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PubMed ID | 10919518 |
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Journal | Res Microbiol |
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Year | 2000 |
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Volume | 151 |
---|
Pages | 383-91 |
---|
Authors | Gennaro PD, Galli E, Orsini F, Pelizzoni F, Sello G, Bestetti G |
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Title | Development of biocatalysts carrying naphthalene dioxygenase and dihydrodiol dehydrogenase genes inducible in aerobic and anaerobic conditions. |
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[13] |
---|
PubMed ID | 11849939 |
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Journal | Curr Opin Biotechnol |
---|
Year | 2001 |
---|
Volume | 12 |
---|
Pages | 564-73 |
---|
Authors | Boyd DR, Sharma ND, Allen CC |
---|
Title | Aromatic dioxygenases: molecular biocatalysis and applications. |
---|
[14] |
---|
PubMed ID | 11056161 |
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Journal | J Biol Chem |
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Year | 2001 |
---|
Volume | 276 |
---|
Pages | 1945-53 |
---|
Authors | Wolfe MD, Parales JV, Gibson DT, Lipscomb JD |
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Title | Single turnover chemistry and regulation of O2 activation by the oxygenase component of naphthalene 1,2-dioxygenase. |
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[15] |
---|
PubMed ID | 11641767 |
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Journal | J Ind Microbiol Biotechnol |
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Year | 2001 |
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Volume | 27 |
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Pages | 94-103 |
---|
Authors | Yu CL, Parales RE, Gibson DT |
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Title | Multiple mutations at the active site of naphthalene dioxygenase affect regioselectivity and enantioselectivity. |
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[16] |
---|
PubMed ID | 12189839 |
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Journal | Chem Commun (Camb) |
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Year | 2002 |
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Volume | (14) |
---|
Pages | 1452-3 |
---|
Authors | Boyd DR, Sharma ND, Kennedy MA, Shepherd SD, Malone JF, Alves-Areias A, Holt R, Allenmark SG, Lemurell MA, Dalton H, Luckarift H |
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Title | Enzyme-catalysed oxygenation and deoxygenation routes to chiral thiosulfinates. |
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[17] |
---|
PubMed ID | 12783560 |
---|
Journal | J Am Chem Soc |
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Year | 2003 |
---|
Volume | 125 |
---|
Pages | 7056-66 |
---|
Authors | Yang TC, Wolfe MD, Neibergall MB, Mekmouche Y, Lipscomb JD, Hoffman BM |
---|
Title | Substrate binding to NO-ferro-naphthalene 1,2-dioxygenase studied by high-resolution Q-band pulsed 2H-ENDOR spectroscopy. |
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[18] |
---|
PubMed ID | 12695887 |
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Journal | J Ind Microbiol Biotechnol |
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Year | 2003 |
---|
Volume | 30 |
---|
Pages | 271-8 |
---|
Authors | Parales RE |
---|
Title | The role of active-site residues in naphthalene dioxygenase. |
---|
[19] |
---|
Comments | X-ray crystallography |
---|
PubMed ID | 12586937 |
---|
Journal | Science |
---|
Year | 2003 |
---|
Volume | 299 |
---|
Pages | 1039-42 |
---|
Authors | Karlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S |
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Title | Crystal structure of naphthalene dioxygenase: side-on binding of dioxygen to iron. |
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Related PDB | 1ndo,1o7g,1o7h,1o7m,1o7n,1o7p,1o7w |
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[20] |
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PubMed ID | 12586930 |
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Journal | Science |
---|
Year | 2003 |
---|
Volume | 299 |
---|
Pages | 1024-5 |
---|
Authors | Kovacs JA |
---|
Title | Biochemistry. How iron activates O2. |
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[21] |
---|
PubMed ID | 15042436 |
---|
Journal | J Biol Inorg Chem |
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Year | 2004 |
---|
Volume | 9 |
---|
Pages | 439-52 |
---|
Authors | Bassan A, Blomberg MR, Siegbahn PE |
---|
Title | A theoretical study of the cis-dihydroxylation mechanism in naphthalene 1,2-dioxygenase. |
---|
[22] |
---|
PubMed ID | 15942729 |
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Journal | J Biol Inorg Chem |
---|
Year | 2005 |
---|
Volume | 10 |
---|
Pages | 483-9 |
---|
Authors | Karlsson A, Parales JV, Parales RE, Gibson DT, Eklund H, Ramaswamy S |
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Title | NO binding to naphthalene dioxygenase. |
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Related PDB | 1uuv,1uuw |
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comments | This enzyme belongs to a large family of bacterial Rieske non-heme iron oxygenases. This enzyme is a part of naphthalene 1,2-dioxygenase system (NDOS). Although NADH and NAD+ are included as a substrate and a product, respectively, they do not interact directly with this enzyme. According to the literature [4], [7], [14] and [18], the reaction proceeds as follows: (#) Ferredoxin-NAD+ reductase (cf. D00071 in EzCatDB) of NDOS catalyzes electron transfer from NADH to Ferredoxin of NDOS. (A) Electron transfer from Ferredoxin to the FE2S2 (Iron-sulfur) of the oxidized form of this enzyme. (A1) Indirect transfer through Trp211 from the adjacent alpha-subunit and Val100, to Cys101, which is bound to FE2S2 (see [4]). (B) Electron transfer from the FE2S2 to the mononuclear iron center of the adjacent subunit of this enzyme. (B1) Indirect transfer through His104 bound to the FE2S2, the sidechain of Asp205 from the adjacent alpha-subunit, and His208 bound to the mononuclear iron center from the adjacent alpha-subunit (see [4] and [7]). (C) Oxygenation of naphthalene at the mononuclear iron center.
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created | updated |
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2005-05-31 | 2018-04-23 |
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