The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7

Tomomi Fujii, Yasuo Hata, Masato Oozeki, Hideaki Moriyama, Takayoshi Wakagi, Nobuo Tanaka, Tairo Oshima

Research output: Contribution to journalArticle

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Abstract

The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 Å resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The 'core fold' part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two α- helices near the clusters, and two sheets of two-stranded antiparallel β- sheet (the terminal and central β-sheets). The 'N-terminal extension' part is mainly formed by a one-turn α-helix and a three-stranded antiparallel β- sheet. The β-sheet in the N-terminal extension is hydrogen-bonded with the terminal β-sheet in the core fold to form a larger β-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the β-sheet in the N-terminal extension and the central β-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.

Original languageEnglish (US)
Pages (from-to)1505-1513
Number of pages9
JournalBiochemistry
Volume36
Issue number6
DOIs
StatePublished - Feb 11 1997

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Sulfolobus
Ferredoxins
Archaea
Zinc
Crystal structure
Ions
Iron
Amino Acids
Atoms
Structural Models
Ligation
Hydrogen
Scattering
Peptides
Molecules
Water

ASJC Scopus subject areas

  • Biochemistry

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The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7. / Fujii, Tomomi; Hata, Yasuo; Oozeki, Masato; Moriyama, Hideaki; Wakagi, Takayoshi; Tanaka, Nobuo; Oshima, Tairo.

In: Biochemistry, Vol. 36, No. 6, 11.02.1997, p. 1505-1513.

Research output: Contribution to journalArticle

Fujii, Tomomi ; Hata, Yasuo ; Oozeki, Masato ; Moriyama, Hideaki ; Wakagi, Takayoshi ; Tanaka, Nobuo ; Oshima, Tairo. / The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7. In: Biochemistry. 1997 ; Vol. 36, No. 6. pp. 1505-1513.
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abstract = "The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 {\AA} resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The 'core fold' part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two α- helices near the clusters, and two sheets of two-stranded antiparallel β- sheet (the terminal and central β-sheets). The 'N-terminal extension' part is mainly formed by a one-turn α-helix and a three-stranded antiparallel β- sheet. The β-sheet in the N-terminal extension is hydrogen-bonded with the terminal β-sheet in the core fold to form a larger β-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the β-sheet in the N-terminal extension and the central β-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.",
author = "Tomomi Fujii and Yasuo Hata and Masato Oozeki and Hideaki Moriyama and Takayoshi Wakagi and Nobuo Tanaka and Tairo Oshima",
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T1 - The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7

AU - Fujii, Tomomi

AU - Hata, Yasuo

AU - Oozeki, Masato

AU - Moriyama, Hideaki

AU - Wakagi, Takayoshi

AU - Tanaka, Nobuo

AU - Oshima, Tairo

PY - 1997/2/11

Y1 - 1997/2/11

N2 - The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 Å resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The 'core fold' part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two α- helices near the clusters, and two sheets of two-stranded antiparallel β- sheet (the terminal and central β-sheets). The 'N-terminal extension' part is mainly formed by a one-turn α-helix and a three-stranded antiparallel β- sheet. The β-sheet in the N-terminal extension is hydrogen-bonded with the terminal β-sheet in the core fold to form a larger β-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the β-sheet in the N-terminal extension and the central β-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.

AB - The crystal structure of ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7 was determined by multiple isomorphous replacement supplemented with anomalous scattering effects of iron atoms in the Fe-S clusters, and refined at 2.0 Å resolution to a crystallographic R value of 0.173. The structural model contains a polypeptide chain of 103 amino acid residues, 2 [3Fe-4S] clusters, and 31 water molecules; in this model, the cluster corresponding to cluster II in bacterial dicluster ferredoxins loses the fourth iron atom although it may originally be a [4Fe-4S] cluster. The structure of the archaeal ferredoxin consists of two parts: the core fold part (residues 37-103) and the N-terminal extension part (residues 1-36). The 'core fold' part has an overall main-chain folding common to bacterial dicluster ferredoxins, containing two clusters as the active center, two α- helices near the clusters, and two sheets of two-stranded antiparallel β- sheet (the terminal and central β-sheets). The 'N-terminal extension' part is mainly formed by a one-turn α-helix and a three-stranded antiparallel β- sheet. The β-sheet in the N-terminal extension is hydrogen-bonded with the terminal β-sheet in the core fold to form a larger β-sheet. The distinct structural feature of this archaeal ferredoxin lies in the zinc-binding center where the zinc ion is tetrahedrally ligated by four amino acid residues (His 16, His 19, and His 34 from the N-terminal extension, and Asp 76 from the core fold). The zinc ion in the zinc-binding center is located at the interface between the core fold and the N-terminal extension, and connects the β-sheet in the N-terminal extension and the central β-sheet in the core fold through the zinc ligation. Thus, the zinc ion plays an important role in stabilizing the structure of the present archaeal ferredoxin by connecting the N-terminal extension and the core fold, which may be common to thermoacidophilic archaeal ferredoxins.

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