Catalytic Mechanism of Retaining α-Galactosidase Belonging to Glycoside Hydrolase Family 97

Journal of Molecular Biology

Volumn 392, Issue 5, 2009, Pages 1232-1241

  Okuyama, Masayuki ^a   Kitamura, Momoyo ^a   Hondoh, Hironori ^a   Kang, Min Sun ^a   Mori, Haruhide ^a   Kimura, Atsuo ^a   Tanaka, Isao ^a   Yao, Min ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

arrangement of catalytic residues; catalytic mechanism; glycoside hydrolase family 97; retaining galactosidase; three dimensional structure

Indexed keywords

ALPHA GALACTOSIDASE; AMINO ACID; ASPARTIC ACID; AZIDE; CARBON; GLYCOSIDASE; PROTEIN GH97A; PROTEIN GH97B; UNCLASSIFIED DRUG; WATER;

AMINO ACID SEQUENCE; ARTICLE; BACTEROIDES THETAIOTAOMICRON; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME INACTIVATION; ENZYME LOCALIZATION; ENZYME MECHANISM; ENZYME SUBSTRATE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FAMILY; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS;

BACTEROIDES THETAIOTAOMICRON;

ALPHA-GALACTOSIDASE; AMINO ACID SEQUENCE; BACTEROIDES; BIOCATALYSIS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; GLYCOSIDE HYDROLASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, TERTIARY;

EID: 70149118733     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.07.068     Document Type: Article

References (24)

1. Cantarel B., Coutinho P., Rancurel C., Bernard T., Lombard V., and Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37 (2009) D233-D238
2. Henrissat B. A classification of glycosyl hydrolases based on amino-acid-sequence similarities. Biochem. J. 280 (1991) 309-316
3. Henrissat B., and Bairoch A. New families in the classification of glycosyl hydrolases based on amino-acid-sequence similarities. Biochem. J. 293 (1993) 781-788
4. Gloster T., Turkenburg J., Potts J., Henrissat B., and Davies G. Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora. Chem. Biol. 15 (2008) 1058-1067
5. Kitamura M., Okuyama M., Tanzawa F., Mori H., Kitago Y., Watanabe N., et al. Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J. Biol. Chem. 283 (2008) 36328-36337
6. Zechel D., and Withers S. Dissection of nucleophilic and acid-base catalysis in glycosidases. Curr. Opin. Chem. Biol. 5 (2001) 643-649
7. Matthews B. Solvent content of protein crystals. J. Mol. Biol. 33 (1968) 491-497
8. Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
9. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (1998), W.H. Freeman and Company, New York, NY
10. Joshi M., Sidhu G., Pot I., Brayer G., Withers S., and McIntosh L. Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J. Mol. Biol. 299 (2000) 255-279
11. Vocadlo D., Wicki J., Rupitz K., and Withers S. A case for reverse protonation: identification of Glu160 as an acid/base catalyst in Thermoanaerobacterium saccharolyticum β-xylosidase and detailed kinetic analysis of a site-directed mutant. Biochemistry 41 (2002) 9736-9746
12. Rigden D. Iterative database searches demonstrate that glycoside hydrolase families 27, 31, 36 and 66 share a common evolutionary origin with family 13. FEBS Lett. 523 (2002) 17-22
13. Janecek S., Svensson B., and MacGregor E. A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEBS Lett. 581 (2007) 1261-1268
14. Todd A., Orengo C., and Thornton J. Plasticity of enzyme active sites. Trends Biochem. Sci. 27 (2002) 419-426
15. Kuroki R., Weaver L., and Matthews B. Structural basis of the conversion of T4 lysozyme into a transglycosidase by reengineering the active site. Proc. Natl Acad. Sci. USA 96 (1999) 8949-8954
16. Hancock S., Vaughan M., and Withers S. Engineering of glycosidases and glycosyltransferases. Curr. Opin. Chem. Biol. 10 (2006) 509-519
17. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
18. Bailey S. The CCP4 suite-programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50 (1994) 760-763
19. Laskowski R., Macartur M., Moss D., and Thornton J. PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
20. Navaza J. AMORE-an automated package for molecular replacement. Acta Crystallogr., Sect. A: Found. Crystallogr. 50 (1994) 157-163
21. Brunger A., Adams P., Clore G., DeLano W., Gros P., Grosse-Kunstleve R., et al. Crystallography & NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921
22. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60 (2004) 2126-2132
23. Datta A. Efficient amplification using 'megaprimer' by asymmetric polymerase chain reaction. Nucleic Acids Res. 23 (1995) 4530-4531
24. Biegert A., Mayer C., Remmert M., Söding J., and Lupas A. The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res. 34 (2006) W335-W339