Fujii T, Hata Y, Oozeki M, Moriyama H, Wakagi T, Tanaka N, Oshima T
Institute for Chemical Research, Kyoto University, Uji, Japan.
Biochemistry. 1997 Feb 11;36(6):1505-13. doi: 10.1021/bi961966j.
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 A 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 alpha-helices near the clusters, and two sheets of two-stranded antiparallel beta-sheet (the terminal and central beta-sheets). The "N-terminal extension" part is mainly formed by a one-turn alpha-helix and a three-stranded antiparallel beta-sheet. The beta-sheet in the N-terminal extension is hydrogen-bonded with the terminal beta-sheet in the core fold to form a larger beta-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 beta-sheet in the N-terminal extension and the central beta-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.
嗜热嗜酸古菌硫磺矿硫化叶菌菌株7铁氧化还原蛋白的晶体结构通过多同晶置换法并辅以铁硫簇中铁原子的反常散射效应得以确定，并在2.0埃分辨率下精修至晶体学R值为0.173。结构模型包含一条由103个氨基酸残基组成的多肽链、2个[3Fe - 4S]簇和31个水分子；在该模型中，对应于细菌双簇铁氧化还原蛋白中簇II的簇虽原本可能是一个[4Fe - 4S]簇，但失去了第四个铁原子。古菌铁氧化还原蛋白的结构由两部分组成：核心折叠部分（残基37 - 103）和N端延伸部分（残基1 - 36）。“核心折叠”部分具有细菌双簇铁氧化还原蛋白共有的整体主链折叠，包含两个作为活性中心的簇、簇附近的两个α螺旋以及两片双链反平行β折叠（末端和中央β折叠）。“N端延伸”部分主要由一个单圈α螺旋和一个三链反平行β折叠形成。N端延伸部分的β折叠与核心折叠中的末端β折叠通过氢键相连形成一个更大的β折叠。这种古菌铁氧化还原蛋白独特的结构特征在于锌结合中心，其中锌离子由四个氨基酸残基（来自N端延伸部分的His 16、His 19和His 34，以及来自核心折叠的Asp 76）以四面体方式配位。锌结合中心的锌离子位于核心折叠和N端延伸部分的界面处，并通过锌配位连接N端延伸部分的β折叠和核心折叠中的中央β折叠。因此，锌离子通过连接N端延伸部分和核心折叠在稳定当前古菌铁氧化还原蛋白的结构中发挥重要作用，这可能是嗜热嗜酸古菌铁氧化还原蛋白共有的特征。
