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研究生:許富源
研究生(外文):Fu-Yuan Hsu
論文名稱:四個β-jellyroll 醣水解酶家族的結構及功能分析
論文名稱(外文):Structural and functional analysis of four glycoside hydrolase β-jellyroll families
指導教授:蔡麗珠蔡麗珠引用關係
口試委員:徐唯哲鄭貽生
口試日期:2012-01-09
學位類別:碩士
校院名稱:國立臺北科技大學
系所名稱:有機高分子研究所
學門:工程學門
學類:化學工程學類
論文種類:學術論文
論文出版年:2012
畢業學年度:100
語文別:中文
論文頁數:61
中文關鍵詞:醣苷水解酶β-jellyroll 家族保留胺基酸三級結構與一級序列比對
外文關鍵詞:glycoside hydrolase β-jellyroll familyconserved amino acidstructural and
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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

1.Cantarel, B.L., et al., The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Research, 2009. 37(Database): p. D233-D238.
2.Ducros, V.M.A., et al., Anatomy of GlycosynthesisStructure and Kinetics of the Humicola insolens Cel7B E197A and E197S Glycosynthase Mutants. Chemistry & Biology, 2003. 10(7): p. 619-628.
3.Knowles, J.K.C., et al., Stereochemical course of the action of the cellobioside hydrolases I and II of Trichoderma reesei. Journal of the Chemical Society, Chemical Communications, 1988(21): p. 1401-1402.
4.Kuhls, K., et al., Molecular evidence that the asexual industrial fungus Trichoderma reesei is a clonal derivative of the ascomycete Hypocrea jecorina. Proc Natl Acad Sci U S A, 1996. 93(8755548): p. 7755-7760.
5.Divne, C., et al., The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei. Science, 1994. 265(8036495): p. 524-528.
6.Ståhlberg, J., et al., Activity Studies and Crystal Structures of Catalytically Deficient Mutants of Cellobiohydrolase I fromTrichoderma reesei. Journal of Molecular Biology, 1996. 264(2): p. 337-349.
7.MacKenzie, L.F., et al., Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 Å resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate. Biochem J, 1998. 335 ( Pt 2)(9761741): p. 409-416.
8.Ducros, V.M.A., et al., Anatomy of Glycosynthesis: Structure and Kinetics of the Humicola insolens Cel7B E197A and E197S Glycosynthase Mutants. Chemistry & Biology, 2003. 10(7): p. 619-628.
9.Klarskov, K., et al., Cellobiohydrolase I from Trichoderma reesei: Identification of an active-site nucleophile and additional information on sequence including the glycosylation pattern of the core protein. Carbohydrate Research, 1997. 304(2): p. 143-154.
10.Sulzenbacher, G., M. Schülein, and G.J. Davies, Structure of the Endoglucanase I from Fusarium oxysporum:  Native, Cellobiose, and 3,4-Epoxybutyl b-D-Cellobioside-Inhibited Forms, at 2.3 Å Resolution. Biochemistry, 1997. 36(19): p. 5902-5911.
11.Viladot, J.-L., et al., Probing the Mechanism of Bacillus 1,3-1,4-b-D-Glucan 4-Glucanohydrolases by Chemical Rescue of Inactive Mutants at Catalytically Essential Residues. Biochemistry, 1998. 37(32): p. 11332-11342.
12.Sulzenbacher, G., et al., Structure of the Fusarium oxysporum Endoglucanase I with a Nonhydrolyzable Substrate Analogue:  Substrate Distortion Gives Rise to the Preferred Axial Orientation for the Leaving Group. Biochemistry, 1996. 35(48): p. 15280-15287.
13.Divne, C., et al., High-resolution crystal structures reveal how a cellulose chain is bound in the 50 Å long tunnel of cellobiohydrolase I from Trichoderma reesei. Journal of Molecular Biology, 1998. 275(2): p. 309-325.
14.Ubhayasekera, W., et al., Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors. FEBS Journal, 2005. 272(8): p. 1952-1964.
15.Parkkinen, T., et al., Crystal structures of Melanocarpus albomyces cellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding. Protein Science, 2008. 17(8): p. 1383-1394.
16.Wicki, J., et al., Recruitment of Both Uniform and Differential Binding Energy in Enzymatic Catalysis:  Xylanases from Families 10 and 11. Biochemistry, 2007. 46(23): p. 6996-7005.
17.Miao, S., et al., Identification of Glutamic Acid 78 as the Active Site Nucleophile in Bacillus subtilis Xylanase Using Electrospray Tandem Mass Spectrometry. Biochemistry, 1994. 33(23): p. 7027-7032.
18.Lawson, S.L., W.W. Wakarchuk, and S.G. Withers, Effects of both Shortening and Lengthening the Active Site Nucleophile of Bacillus circulans Xylanase on Catalytic Activity+. Biochemistry, 1996. 35(31): p. 10110-10118.
19.MacLeod, A.M., et al., The Acid/Base Catalyst in the Exoglucanase/Xylanase from Cellulomonas fimi Is Glutamic Acid 127: Evidence from Detailed Kinetic Studies of Mutants. Biochemistry, 1994. 33(20): p. 6371-6376.
20.McIntosh, L.P., et al., The pKa of the General Acid/Base Carboxyl Group of a Glycosidase Cycles during Catalysis:  A 13C-NMR Study of Bacillus circulans Xylanase. Biochemistry, 1996. 35(31): p. 9958-9966.
21.Wakarchuk, W.W., et al., Mutational and crystallographic analyses of the active site residues of the bacillus circulans xylanase. Protein Science, 1994. 3(3): p. 467-475.
22.Gilbert, H.J., H. Stålbrand, and H. Brumer, How the walls come crumbling down: recent structural biochemistry of plant polysaccharide degradation. Current Opinion in Plant Biology, 2008. 11(3): p. 338-348.
23.Schou, C., et al., Stereochemistry, specificity and kinetics of the hydrolysis of reduced cellodextrins by nine cellulases. European Journal of Biochemistry, 1993. 217(3): p. 947-953.
24.Sulzenbacher, G., et al., The Streptomyces lividans Family 12 Endoglucanase:  Construction of the Catalytic Core, Expression, and X-ray Structure at 1.75 Å Resolution. Biochemistry, 1997. 36(51): p. 16032-16039.
25.Zechel, D.L., et al., Identification of Glu-120 as the catalytic nucleophile in Streptomyces lividans endoglucanase celB. Biochem. J., 1998. 336(1): p. 139-145.
26.Baumann, M.J., et al., Structural Evidence for the Evolution of Xyloglucanase Activity from Xyloglucan Endo-Transglycosylases: Biological Implications for Cell Wall Metabolism. The Plant Cell Online, 2007. 19(6): p. 1947-1963.
27.Malet, C., et al., Stereochemical course and structure of the products of the enzymic action of endo-1,3-1,4-b-D-glucan 4-glucanohydrolase from Bacillus licheniformis. Biochem. J., 1993. 296(3): p. 753-758.
28.Hoj, P., et al., Identification of glutamic acid 105 at the active site of Bacillus amyloliquefaciens 1,3-1,4-b-D-glucan 4-glucanohydrolase using epoxide-based inhibitors. J. Biol. Chem., 1992. 267(35): p. 25059-25066.
29.Antoni, P., Bacterial 1,3-1,4-b-glucanases: structure, function and protein engineering. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 2000. 1543(2): p. 361-382.
30.Keitel, T., et al., Molecular and active-site structure of a Bacillus 1,3-1,4-b-glucanase. Proceedings of the National Academy of Sciences of the United States of America, 1993. 90(11): p. 5287-91.
31.Johansson, P., Crystal Structures of a Poplar Xyloglucan Endotransglycosylase Reveal Details of Transglycosylation Acceptor Binding. The Plant Cell Online, 2004. 16(4): p. 874-886.
32.Ilari, A., et al., Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus– structural basis of substrate recognition. FEBS Journal, 2009. 276(4): p. 1048-1058.
33.Barbeyron, T., et al., The kappa-carrageenase of the marine bacterium Cytophaga drobachiensis. Structural and phylogenetic relationships within family-16 glycoside hydrolases. Molecular Biology and Evolution, 1998. 15(5): p. 528-537.
34.Michel, G., et al., The k-carrageenase of P. carrageenovora Features a Tunnel-Shaped Active Site: A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases. Structure, 2001. 9(6): p. 513-525.
35.Rose, P.W., et al., The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Research, 2010. 39(Database): p. D392-D401.
36.Kleywegt, G.J., et al., The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 Å resolution, and a comparison with related enzymes. Journal of Molecular Biology, 1997. 272(3): p. 383-397.
37.von Ossowski, I., et al., Engineering the Exo-loop of Trichoderma reesei Cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D. Journal of Molecular Biology, 2003. 333(4): p. 817-829.
38.Parkkinen, T., et al., Crystal structures of Melanocarpus albomycescellobiohydrolase Cel7B in complex with cello-oligomers show high flexibility in the substrate binding. Protein Science, 2008. 17(8): p. 1383-1394.
39.Grassick, A., et al., Three-dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterization of the cel7 gene from the filamentous fungus, Talaromyces emersonii. European Journal of Biochemistry, 2004. 271(22): p. 4495-4506.
40.Sabini, E., et al., Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase. Chemistry & Biology, 1999. 6(7): p. 483-492.
41.Yazawa, R., et al., A Calcium-Dependent Xylan-Binding Domain of Alkaline Xylanase from Alkaliphilic Bacillus sp. Strain 41M-1. Bioscience, Biotechnology, and Biochemistry, 2011. 75(2): p. 379-381.
42.Balakrishnan, H., et al., Structural and active site modification studies implicate Glu, Trp and Arg in the activity of xylanase from alkalophilic Bacillus sp. (NCL 87-6-10). Enzyme and Microbial Technology, 2006. 39(1): p. 67-73.
43.Oakley, A.J., et al., Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching. Acta Crystallographica Section D-Biological Crystallography, 2003. 59: p. 627-636.
44.Murakami, M., et al., Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1). FEBS Letters, 2005. 579(28): p. 6505-6510.
45.McCarthy, A.A., et al., Structure of XynB, a highly thermostable b-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 Å resolution. Acta Crystallographica Section D, 2000. 56(11): p. 1367-1375.
46.Wouters, J., et al., Crystallographic analysis of family 11 endo-b-1,4-xylanase Xyl1 from Streptomyces sp S38. Acta Crystallographica Section D-Biological Crystallography, 2001. 57: p. 1813-1819.
47.Hakulinen, N., et al., Three-dimensional structures of thermophilic b-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. European Journal of Biochemistry, 2003. 270(7): p. 1399-1412.
48.Dumon, C., et al., Engineering Hyperthermostability into a GH11 Xylanase Is Mediated by Subtle Changes to Protein Structure. Journal of Biological Chemistry, 2008. 283(33): p. 22557-22564.
49.Fushinobu, S., et al., Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Engineering, 1998. 11(12): p. 1121-1128.
50.Vandermarliere, E., et al., Crystallographic analysis shows substrate binding at the −3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-b-xylanases. Biochemical Journal, 2008. 410(1): p. 71.
51.Jänis, J., et al., Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography. FEBS Journal, 2005. 272(9): p. 2317-2333.
52.Torronen, A. and J. Rouvinen, Sturctural comparison of 2 major endo-1,4-xylanases from Tricoderma-reesei. Biochemistry, 1995. 34(3): p. 847-856.
53.Pompidor, G., et al., A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction. Acta Crystallographica Section D-Biological Crystallography, 2010. 66: p. 762-769.
54.Krengel, U., et al., Crystallization and preliminary crystallographic analysis of endo-1,4-b-xylanase I from Aspergillus niger. Acta Crystallographica Section D-Biological Crystallography, 1996. 52: p. 571-576.
55.Vardakou, M., et al., Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases. Journal of Molecular Biology, 2008. 375(5): p. 1293-1305.
56.Kumar, P.R., et al., The tertiary structure at 1.59 Å resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti Bainier. Journal of Molecular Biology, 2000. 295(3): p. 581-593.
57.Payan, F., The dual nature of the wheat xylanase protein inhibitor XIP-I: structural basis for the inhibition of family 10 and family 11 xylanases. Journal of Biological Chemistry, 2004. 279(34): p. 36029-36037.
58.Michaux, C., et al., Structural insights into the acidophilic pH adaptation of a novel endo-1,4-b-xylanase from Scytalidium acidophilum. Biochimie, 2010. 92(10): p. 1407-1415.
59.Gruber, K., et al., Thermophilic xylanase from Thermomyces lanuginosus: High-resolution X-ray structure and modeling studies. Biochemistry, 1998. 37(39): p. 13475-13485.
60.Moukhametzianov, R., et al., Protein crystallography with a micrometre-sized synchrotron-radiation beam. Acta Crystallographica Section D Biological Crystallography, 2008. 64(2): p. 158-166.
61.Gloster, T.M., et al., Characterization and Three-dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families GH5 and GH12. Journal of Biological Chemistry, 2007. 282(26): p. 19177-19189.
62.Kapoor, D., et al., Replacement of the active surface of a thermophile protein by that of a homologous mesophile protein through structure-guided ‘protein surface grafting’. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, 2008. 1784(11): p. 1771-1776.
63.Sulzenbacher, G., et al., The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 Å resolution. Biochemistry, 1999. 38(15): p. 4826-4833.
64.Sandgren, M., Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability. Protein Science, 2003. 12(4): p. 848-860.
65.Forse, G.J., et al., Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima. Protein Science, 2011. 20(1): p. 168-178.
66.Khademi, S., et al., Determination of the structure of an endoglucanase from Aspergillus niger and its mode of inhibition by palladium chloride. Acta Crystallographica Section D-Biological Crystallography, 2002. 58: p. 660-667.
67.Sandgren, M., et al., Crystal Complex Structures Reveal How Substrate is Bound in the −4 to the +2 Binding Sites of Humicola grisea Cel12A. Journal of Molecular Biology, 2004. 342(5): p. 1505-1517.
68.Sandgren, M., et al., The Humicola grisea Cel12A enzyme structure at 1.2 Å resolution and the impact of its free cysteine residues on thermal stability. Protein Science, 2003. 12(12): p. 2782-2793.
69.Ilari, A., et al., Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus - structural basis of substrate recognition. FEBS Journal, 2009. 276(4): p. 1048-1058.
70.Addington, T., et al., Re-engineering specificity in 1,3-1,4-b-glucanase to accept branched xyloglucan substrates. Proteins: Structure, Function, and Bioinformatics, 2011. 79(2): p. 365-375.
71.Tempel, W., et al., Three-dimesional structure of GlcNAcα1-4Gal releasing Endo-b-Galactosidase from Clostridium perfringens. Proteins: Structure, Function, and Bioinformatics, 2005. 59(1): p. 141-144.
72.Tsai, L.-C., et al., Crystal Structure of Truncated Fibrobacter succinogenes 1,3-1,4-b-D-Glucanase in Complex with b-1,3-1,4-Cellotriose. Journal of Molecular Biology, 2005. 354(3): p. 642-651.
73.Fibriansah, G., et al., The 1.3 Å crystal structure of a novel endo-b-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96. Proteins: Structure, Function, and Bioinformatics, 2007. 69(3): p. 683-690.
74.Gaiser, O., et al., Structural Basis for the Substrate Specificity of a Bacillus 1,3-1,4-b-Glucanase. Journal of Molecular Biology, 2006. 357(4): p. 1211-1225.
75.Michel, G., et al., The kappa-carrageenase of P-carrageenovora features a tunnel-shaped active site: A novel insight in the evolution of clan-B glycoside hydrolases. Structure, 2001. 9(6): p. 513-525.
76.Hong, T.-Y., et al., The 1.5 Å structure of endo-1,3-b-glucanase from Streptomyces sioyaensis: evolution of the active-site structure for 1,3-b-glucan-binding specificity and hydrolysis. Acta Crystallographica Section D, 2008. 64(9): p. 964-970.
77.Hehemann, J.-H., et al., Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature, 2010. 464(7290): p. 908-912.
78.Allouch, J., The Three-dimensional Structures of Two b-Agarases. Journal of Biological Chemistry, 2003. 278(47): p. 47171-47180.
79.Allouch, J., et al., Parallel Substrate Binding Sites in a b-Agarase Suggest a Novel Mode of Action on Double-Helical Agarose. Structure, 2004. 12(4): p. 623-632.
80.Vasur, J., et al., Synthesis of Cyclic b-Glucan Using Laminarinase 16A Glycosynthase Mutant from the Basidiomycete Phanerochaete chrysosporium. Journal of the American Chemical Society, 2010. 132(5): p. 1724-1730.
81.Mark, P., et al., Analysis of nasturtiumTmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucanendo-transglycosylases andendo-hydrolases. Proteins: Structure, Function, and Bioinformatics, 2009. 75(4): p. 820-836.


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