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研究生: 趙悌均
Ti-Chun Chao
論文名稱: 幽門螺旋桿菌無機焦磷酸水解酶晶體結構與功能之研究
Crystal Structure and Functional Studies of Inorganic Pyrophosphatase form Helicobacter pylori
指導教授: 孫玉珠
Yuh-Ju Sun
口試委員:
學位類別: 碩士
Master
系所名稱: 生命科學暨醫學院 - 生物資訊與結構生物研究所
Institute of Bioinformatics and Structural Biology
論文出版年: 2004
畢業學年度: 92
語文別: 英文
論文頁數: 50
中文關鍵詞: 幽門螺旋桿菌無機焦磷酸水解酶晶體結構
外文關鍵詞: Helicobacter pylori, Inorganic pyrophosphatase, crystal structure
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  • 幽門螺旋桿菌是屬於革蘭氏陰性的微好氧細菌, 目前已被證實與胃潰瘍、胃癌及慢性胃炎的引發有相當的關聯性。無機焦磷酸水解酶是細胞內能量代謝的重要酵素之一;此酵素會將在生物聚合物聚成過程中所產生的焦磷酸水解成磷酸,這個反應在熱力學上提供了聚合物形成的趨動力。幽門螺旋桿菌的無機焦磷酸水解酶的分子量大約20 kDa,在分類上是屬於第一族的焦磷酸水解酶,並且他的活化高度仰賴與二價金屬的鍵結。我們藉由膠體過濾層析法和分析型超高速離心機來測定蛋白質在溶液中的四級結構狀態,結果傾向於六元體;在晶體結構分析上也觀察到同樣的結果。 本篇解出了無機焦磷酸水解酶以及與受質焦磷酸鍵結的結構,整個蛋白質結構是由兩個 α螺旋和八個β摺板所組成。一方面分析活化位置的結構與特性,另一方面我們也將大腸桿菌和幽門螺旋桿菌的焦磷酸水解酶作比較,分析他們的不同處。.


    Helicobacter pylori ( H. pylori ) is a gram-negative microaerophilic bacterium that is associated with peptic ulcers, gastric cancer and chronic gastritis. Inorganic pyrophosphatase [E.C.3.6.1.1.] (PPase) is an essential enzyme for energy metabolism in all cells. It catalyzes the hydrolysis of PPi that is synthesized during polymer synthesis and then hydrolyzed to Pi, thus providing a thermodynamic pull favoring polymer synthesis. PPases are strongly dependent on divalent cations. The crystal structure of recombinant PPase from H. pylori (strain: 26695) was reported here. PPase from H. pylori is cytoplasmic and belongs to family I. The molecular weight of H. pylori PPase monomer is about 20 kD. H. pylori PPase is recognized as a hexamer in solution according to the results of ultracentrifugation and gel filtration. The hexameric oligomerization was also seen in the structure. Crystal structures of PPase and PPi-PPase complex were solved here using molecular replacement. The overall PPase structure is composed of two extended α-helices and eight β-strands. Meanwhile, the comparison between H. pylori PPase and E. coli PPase was also described here.

    Contents Chapter1 Introduciton 1.1 Preface --------------------------------------- 1 1.2 Inorganic pyrophosphatase --------------------- 2 Chapter2 Material and Methods 2.1 Protein Preparation --------------------------- 5 2.2 Protein Purity Recognition -------------------- 5 2.3 Gel filtration -------------------------------- 5 2.4 Analytical Ultracentrifugation ---------------- 6 2.5 Crystallization of PPase ---------------------- 6 2.6 Crystallization of PPi-PPase Complex -------- 7 2.7 X-ray Diffraction Data Collection ------------- 7 2.8 Molecular Replacement ------------------------- 8 2.9 Model Building and Refinement ----------------- 9 Chapter 3 Results 3.1 Sequence alignment --------------------------- 11 3.2 Characterization ------------------------------ 11 3.3 Space Group Determination --------------------- 12 3.4 Phase determination of PPase ------------------ 13 3.5 Phase determination of PPi-PPase complex ------ 14 3.6 Quality of the PPase model -------------------- 14 3.7 Quality of the PPi-PPase complex model ------- 15 3.8 PPi identification ---------------------------- 15 3.9 Overall structure of PPase -------------------- 16 3.10 Oligomeric structure of PPase ---------------- 16 Chapter 4 Discussion 4.1 The active site ------------------------------- 18 4.2 Comparison between H. pylori PPase and EPPase 19 4.3 Metal binding --------------------------------- 19 4.4 Pyrophosphate binding ------------------------- 20 Figures and Figure Legends -------------------------- 22 Tables ---------------------------------------------- 41 References ------------------------------------------ 48

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