臺灣博碩士論文加值系統

從醣苷水解酶資料庫中的得知第 7、11、12 和16 四個家族中蛋白質的三級結構都擁有捲心狀β-sandwich 的類似立體結構。然而從胺基酸序列排序比對的結果顯示，它們之間的差異性很大，但是它們卻擁有非常相似催化活性區域。本篇論文的研究目標為從已知蛋白質三級結構為出發點，並與其它相似功能的結構做細部比對與討論。利用重疊的立體結構為基礎來比對胺基酸序列的相對位置，得知序列保留RYYDQDNExDxEHFWWYP 及ExDxE/ExDxxE的序列通式(regular expression)分別於第7和16家族的活性區域中，而第11、12 家族則是分別有YWEnYPFQEn+(88~94)和NWYEnMWPEn+(83~97)保留特性。其中第一個與最後一個麩胺酸（E）就是分別扮演催化活性的親核性和當一般酸/鹼的兩個主要催化胺基酸，而且在空間位置上這四個家族都互相對應到。從分析數據得知第16 家族中蛋白質胺基酸序列平均相同度約為22%左右，是四個不同家族中差異最大，但其蛋白質立體結構與核心催化活性胺基酸位置卻有相當高的相似性。

The three-dimensional (3D) structure of glycoside hydrolase family (GHF) 7, 11, 12 and 16 are collectively referred to as a jellyroll β-sandwich fold with a similar cleft catalytic active site,although the amino acid sequences of these four families are diverse. Based on the results of
primary sequence alignment and 3D structural comparison, GHF 7 and 16 possess a conserved catalytic motif of RYYDQDNExDxEHFWWYP and ExDxE/ExDxxE, whereas GHF11 and 12
share a general active site motif of YWEnYPFQEn+(88~94) and NWYEnMWPEn+(83~97), respectively. The first and last glutamyl residues found in the catalytic motifs have been clearly identified as catalytic nucleophile and general acid/base for retention hydrolytic mechanism, respectively. A detailed structural comparison among the known structures reveals that they share a low level of amino acid sequence identity about 22%, but the enzymes have a high degree of structural conservation at the active sites.

摘要 ................................ I
ABSTRACT ............................ II
誌謝 ................................ III
目錄 ................................ IV
圖目錄 .............................. VI
表目錄 .............................. VIII
縮寫表 .............................. IX
第 1 章 前言 ........................ 1
1.1. 醣水解酶介紹 ................... 1
1.2. 醣水解酶第7 家族 ............... 4
1.3. 醣水解酶第11 家族 .............. 8
1.4. 醣水解酶第12 家族 .............. 10
1.5. 醣水解酶第16 家族 .............. 12
1.6. 研究動機 ....................... 15
第 2 章 資料來源與使用工具 .......... 16
2.1. CAZy ........................... 16
2.2. Protein Data Bank .............. 17
2.3. SALIGN ......................... 18
2.4. ClustalW2 ...................... 19
2.5. Treeview ....................... 21
2.6. Pymol .......................... 22
2.7. Accelry Discovery Studio ....... 22
2.8. WebLogo ........................ 24
2.9. 方法 ........................... 26
第 3 章 實驗結果 .................... 28
3.1. 醣水解酶第7 家族分析 ........... 28
3.2. 醣水解酶第11 家族分析 .......... 32
3.3. 醣水解酶第12 家族分析 .......... 38
3.4. 醣水解酶第16 家族分析 .......... 42
3.5. 醣水解酶四個家族比較 ........... 47
第 4 章 結論與討論 .................. 52
參考文獻 ............................ 54
附錄 ................................ 60

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