Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system

Jeong Won Nam, Haruko Noguchi, Zui Fujimoto, Hiroshi Mizuno, Yuji Ashikawa, Mitsuru Abo, Shinya Fushinobu, Nobuyuki Kobashi, Takayoshi Wakagi, Kenichi Iwata, Takako Yoshida, Hiroshi Habe, Hisakazu Yamane, Toshio Omori, Hideaki Nojiri

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 Å resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three β-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.

Original languageEnglish
Pages (from-to)779-789
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume58
Issue number4
DOIs
Publication statusPublished - 2005 Mar 1
Externally publishedYes

Fingerprint

Ferredoxins
Oxygenases
Fluorouracil
Iron
Crystal structure
biphenyl-2,3-dioxygenase
Carbon
Electric charge
Electrons
carbazole 1,9a-dioxygenase
Oxidoreductases
Proteins
Nitrogen
Atoms

Keywords

  • 2Fe-2S cluster
  • Angular dioxygenase
  • Angular dioxygenation
  • Biodegradation
  • CarAc
  • Electron transport protein
  • Rieske ferredoxin
  • Rieske non-heme iron oxygenase system
  • Rieske-type protein

ASJC Scopus subject areas

  • Genetics
  • Structural Biology
  • Biochemistry

Cite this

Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system. / Nam, Jeong Won; Noguchi, Haruko; Fujimoto, Zui; Mizuno, Hiroshi; Ashikawa, Yuji; Abo, Mitsuru; Fushinobu, Shinya; Kobashi, Nobuyuki; Wakagi, Takayoshi; Iwata, Kenichi; Yoshida, Takako; Habe, Hiroshi; Yamane, Hisakazu; Omori, Toshio; Nojiri, Hideaki.

In: Proteins: Structure, Function and Genetics, Vol. 58, No. 4, 01.03.2005, p. 779-789.

Research output: Contribution to journalArticle

Nam, JW, Noguchi, H, Fujimoto, Z, Mizuno, H, Ashikawa, Y, Abo, M, Fushinobu, S, Kobashi, N, Wakagi, T, Iwata, K, Yoshida, T, Habe, H, Yamane, H, Omori, T & Nojiri, H 2005, 'Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system', Proteins: Structure, Function and Genetics, vol. 58, no. 4, pp. 779-789. https://doi.org/10.1002/prot.20374
Nam, Jeong Won ; Noguchi, Haruko ; Fujimoto, Zui ; Mizuno, Hiroshi ; Ashikawa, Yuji ; Abo, Mitsuru ; Fushinobu, Shinya ; Kobashi, Nobuyuki ; Wakagi, Takayoshi ; Iwata, Kenichi ; Yoshida, Takako ; Habe, Hiroshi ; Yamane, Hisakazu ; Omori, Toshio ; Nojiri, Hideaki. / Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system. In: Proteins: Structure, Function and Genetics. 2005 ; Vol. 58, No. 4. pp. 779-789.
@article{ff84666ee0f8456fa2dcfc5f1b6db829,
title = "Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system",
abstract = "The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 {\AA} resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three β-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.",
keywords = "2Fe-2S cluster, Angular dioxygenase, Angular dioxygenation, Biodegradation, CarAc, Electron transport protein, Rieske ferredoxin, Rieske non-heme iron oxygenase system, Rieske-type protein",
author = "Nam, {Jeong Won} and Haruko Noguchi and Zui Fujimoto and Hiroshi Mizuno and Yuji Ashikawa and Mitsuru Abo and Shinya Fushinobu and Nobuyuki Kobashi and Takayoshi Wakagi and Kenichi Iwata and Takako Yoshida and Hiroshi Habe and Hisakazu Yamane and Toshio Omori and Hideaki Nojiri",
year = "2005",
month = "3",
day = "1",
doi = "10.1002/prot.20374",
language = "English",
volume = "58",
pages = "779--789",
journal = "Proteins: Structure, Function and Genetics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "4",

}

TY - JOUR

T1 - Crystal structure of the ferredoxin component of carbazole 1,9a-dioxygenase of Pseudomonas resinovorans strain CA10, a novel Rieske non-heme iron oxygenase system

AU - Nam, Jeong Won

AU - Noguchi, Haruko

AU - Fujimoto, Zui

AU - Mizuno, Hiroshi

AU - Ashikawa, Yuji

AU - Abo, Mitsuru

AU - Fushinobu, Shinya

AU - Kobashi, Nobuyuki

AU - Wakagi, Takayoshi

AU - Iwata, Kenichi

AU - Yoshida, Takako

AU - Habe, Hiroshi

AU - Yamane, Hisakazu

AU - Omori, Toshio

AU - Nojiri, Hideaki

PY - 2005/3/1

Y1 - 2005/3/1

N2 - The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 Å resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three β-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.

AB - The carbazole 1,9a-dioxygenase (CARDO) system of Pseudomonas resinovorans strain CA10 catalyzes the dioxygenation of carbazole; the 9aC carbon bonds to a nitrogen atom and its adjacent 1C carbon as the initial reaction in the mineralization pathway. The CARDO system is composed of ferredoxin reductase (CarAd), ferredoxin (CarAc), and terminal oxygenase (CarAa). CarAc acts as a mediator in the electron transfer from CarAd to CarAa. To understand the structural basis of the protein-protein interactions during electron transport in the CARDO system, the crystal structure of CarAc was determined at 1.9 Å resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three β-sheets, and the structure can be divided into two domains, a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF, and the distribution of electric charge on its molecular surface is very different. Such differences are thought to explain why these ferredoxins can act as electron mediators in respective electron transport chains composed of different-featured components.

KW - 2Fe-2S cluster

KW - Angular dioxygenase

KW - Angular dioxygenation

KW - Biodegradation

KW - CarAc

KW - Electron transport protein

KW - Rieske ferredoxin

KW - Rieske non-heme iron oxygenase system

KW - Rieske-type protein

UR - http://www.scopus.com/inward/record.url?scp=13944256249&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=13944256249&partnerID=8YFLogxK

U2 - 10.1002/prot.20374

DO - 10.1002/prot.20374

M3 - Article

C2 - 15645447

AN - SCOPUS:13944256249

VL - 58

SP - 779

EP - 789

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - 4

ER -