1eg9
From Proteopedia
(New page: 200px<br /><applet load="1eg9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eg9, resolution 1.60Å" /> '''NAPHTHALENE 1,2-DIOX...) |
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| - | [[Image:1eg9.jpg|left|200px]]<br /><applet load="1eg9" size=" | + | [[Image:1eg9.jpg|left|200px]]<br /><applet load="1eg9" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1eg9, resolution 1.60Å" /> | caption="1eg9, resolution 1.60Å" /> | ||
'''NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.'''<br /> | '''NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The three-dimensional structure of the aromatic hydroxylating enzyme | + | The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products. |
==About this Structure== | ==About this Structure== | ||
| - | 1EG9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with SO4, FE, FES and IND as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Naphthalene_1,2-dioxygenase Naphthalene 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.12 1.14.12.12] Full crystallographic information is available from [http:// | + | 1EG9 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=FE:'>FE</scene>, <scene name='pdbligand=FES:'>FES</scene> and <scene name='pdbligand=IND:'>IND</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Naphthalene_1,2-dioxygenase Naphthalene 1,2-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.12 1.14.12.12] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EG9 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Choudhury, D.]] | [[Category: Choudhury, D.]] | ||
[[Category: Eklund, H.]] | [[Category: Eklund, H.]] | ||
| - | [[Category: Gibson, D | + | [[Category: Gibson, D T.]] |
[[Category: Karlsson, A.]] | [[Category: Karlsson, A.]] | ||
[[Category: Kauppi, B.]] | [[Category: Kauppi, B.]] | ||
[[Category: Lee, K.]] | [[Category: Lee, K.]] | ||
| - | [[Category: Parales, J | + | [[Category: Parales, J V.]] |
| - | [[Category: Parales, R | + | [[Category: Parales, R E.]] |
[[Category: Ramaswamy, S.]] | [[Category: Ramaswamy, S.]] | ||
[[Category: FE]] | [[Category: FE]] | ||
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[[Category: non-heme iron dioxygenase]] | [[Category: non-heme iron dioxygenase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:27:24 2008'' |
Revision as of 10:27, 21 February 2008
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NAPHTHALENE 1,2-DIOXYGENASE WITH INDOLE BOUND IN THE ACTIVE SITE.
Overview
The three-dimensional structure of the aromatic hydroxylating enzyme naphthalene dioxygenase (NDO) from Pseudomonas sp. NCIB 9816-4 was recently determined. The refinement of the structure together with cyclic averaging showed that in the active site of the enzyme there is electron density for a flat aromatic compound. This compound appears to be an indole adduct, which in Escherichia coli is derived from tryptophan present in the rich culture medium. An indole-dioxygen adduct has been built which fits the electron density convincingly. Support for this interpretation was obtained from crystals of the enzyme purified from cells grown in the absence of tryptophan which had an empty substrate pocket. These types of crystals were soaked in indole solutions and the position of indole in this complex was similar to the corresponding part in the modelled indole-oxygen adduct. This suggests that a peroxide bound to iron end-on attacks the substrate and forms this intermediate. The substrate position has implications for the substrate specificity of the enzyme. Docking studies with indole, naphthalene and biphenyl inside the substrate pocket of NDO suggest the presence of subpockets where the one close to the active site iron is reserved for the binding of the aromatic ring which is hydroxylated upon catalysis. The plausible location for the binding of dioxygen is between this pocket and the catalytic iron. This is in accordance with the enantiospecificity of the products.
About this Structure
1EG9 is a Protein complex structure of sequences from Pseudomonas putida with , , and as ligands. Active as Naphthalene 1,2-dioxygenase, with EC number 1.14.12.12 Full crystallographic information is available from OCA.
Reference
Substrate binding site of naphthalene 1,2-dioxygenase: functional implications of indole binding., Carredano E, Karlsson A, Kauppi B, Choudhury D, Parales RE, Parales JV, Lee K, Gibson DT, Eklund H, Ramaswamy S, J Mol Biol. 2000 Feb 18;296(2):701-12. PMID:10669618
Page seeded by OCA on Thu Feb 21 12:27:24 2008
Categories: Naphthalene 1,2-dioxygenase | Protein complex | Pseudomonas putida | Carredano, E. | Choudhury, D. | Eklund, H. | Gibson, D T. | Karlsson, A. | Kauppi, B. | Lee, K. | Parales, J V. | Parales, R E. | Ramaswamy, S. | FE | FES | IND | SO4 | Enzyme-substrate complex | Non-heme iron dioxygenase
