自硫酸鹽還原菌 Desulfovibrio gigas 中三種形式的亞硫酸鹽還原酶之結構與特性探討其催化機制

Structural insights into the enzyme catalysis from comparison of three forms of dissimilatory sulfite reductase from desulfovibrio gigas

謝殷程(Yin-Cheng Hsieh)

指導教授 ： 吳文桂 ； 陳俊榮

國立清華大學/生命科學院/生物資訊與結構生物研究所/博士(2010年)

https://doi.org/10.6843/NTHU.2010.00593

摘要

亞硫酸鹽還原酶在硫酸鹽還原菌中扮演著催化亞硫酸鹽反應成為硫分子的機制。在這個研究中我們解出了硫酸鹽還原菌 Desulfovibrio gigas 中兩種有活性的亞硫酸鹽還原酶﹣Dsr-I （解析度 1.76 A） 和 Dsr-II （解析度 2.05 A） ﹣的晶體結構。結果顯示第一種亞硫酸還原酶是 α2β2γ2 的二分子聚合體 (dimer) 並且含有八個四鐵四硫群，兩個馬鞍形狀的西羅血紅素 (siroheme) 以及兩個 sirohydrochlorin。第一種亞硫酸還原酶的西羅血紅素與四鐵四硫群結合，然而第二種亞硫酸還原酶在這個位置使用了三鐵四硫群取代，並且第二種亞硫酸還原酶裡原本用來鍵結第四個鐵原子的 Cysβ188被Cysβ145 取代。在這兩種亞硫酸還原酶中存在著一條正電荷通道連結西羅血紅素與sirohydrochlorin，我們發現這個通道的開口被 ferredoxin domain 上的一段氨基酸蓋住。在第一種亞硫酸還原酶裡 γ 次單位使用 C 端氨基酸 Cysγ104 深入 α 次單位和 β 次單位形成之正電通道且和西羅血紅素中的 CHA 原子鍵結，然而在第二種亞硫酸還原酶裡這個鍵結被打斷並把 Cysγ104 的琉原子移到西羅血紅素上的亞硫酸鹽附近。除此之外，γ 次單位的 C 端在兩種亞硫酸還原酶裡還存在著 Cysγ93 與 Cysγ104 鍵結的位向。除了活性中心的亞硫酸分子外，我們也發現了 Lysγ100 附件有第二個亞硫酸分子，這個發現使我們對於亞硫酸分子如何進入活性中心有進一步了解。我們也使用電子自旋共振研究亞硫酸還原酶。電子自旋共振圖譜確認了第一種與第二種亞硫酸鹽還原酶晶體結構的結果，但是第三種無活性亞硫酸還原酶在電子自旋共振圖譜中顯示西羅血紅
素不含鐵原子中心，同時它也和第二種亞硫酸還原酶一樣使用三鐵四硫群和去鐵西羅血紅素結合。這三種形式的亞硫酸還原酶結構研究使我們對於硫酸鹽還原過程如何產
生連三硫酸根，硫代硫酸根和硫分子的反應機制有了進一步了解。

關鍵字

亞硫酸 ； 亞硫酸還原酶 ； 結構 ； 晶體

並列摘要

Sulfite reductase mediates the reduction of sulfite to sulfide in sulfate-reducing bacteria. Here, we compare the crystal structures between two distinct forms of the dissimilatory sulfite reductase (Dsr), desulfoviridin, from Desulfovibrio gigas, Dsr-I and Dsr- II, at 1.76 and 2.1 A resolution, respectively. The dimeric α2β2γ2 structure of Dsr-I contains eight [4Fe-4S] clusters, two saddle-shaped sirohemes and two flat sirohydrochlorins. In Dsr- II, the [4Fe-4S] cluster associated with each of the siroheme in Dsr-I is replaced by a [3Fe-4S] cluster. This structural feature allows Thrβ145 to position itself closer to the [3Fe-4S] in Dsr- II to replace the role of the Cysβ188 that ligates the [4Fe-4S] in Dsr-I. In both Dsr forms, each of the sirohydrochlorins is located in a putative substrate channel connected to the siroheme and capped by a dynamic loop from the ferredoxin domain. The γ-subunit C-terminus is inserted into a positively charged channel formed between the α- and β-subunits, with its conserved terminal Cysγ104 side chain covalently linked to the CHA atom of the siroheme in Dsr-I. In Dsr-II, the thiolate bond is broken, and the Cysγ104 side chain moves closer to the
bound sulfite at the siroheme pocket. Moreover, the γ-subunit in the region of the C- terminus reveals another arrangement with an interaction between Cysγ93 and Cysγ104 in both Dsr-I and Dsr-II. Beside the sulfite in the active site, a second sulfite interacting with the conserved Lysγ100 has also been identified, implicating this site as the entry into a putative substrate channel. Electron paramagnetic resonance (EPR) of the active Dsr-I and Dsr-II confirm the co-factor structures, whereas EPR of a third but inactive form, Dsr-III, suggests that the siroheme has been demetallated in addition to its associated [4Fe-4S] cluster replaced by a [3Fe-4S] center. A catalytic mechanism that can lead to S3O62−, S2O32− and S2−, the three distinct products observed in the dissimilatory sulfite reduction, is proposed.

並列關鍵字

sulfite ； sulfite reductase ； structure ； crystal

參考文獻

Crane, B.R., and Getzoff, E.D. (1996) The relationship between structure and

Beinert, H., Holm, R.H., and Munck, E. (1997) Iron-sulfur clusters: nature's modular,

multipurpose structures. Science 277: 653-659.

flavoredoxin gene in Desulfovibrio gigas reveals its participation in thiosulfate

reduction. FEBS Letters 579: 4803-4807.