In silico identification of catalytic residues and domain fold of the family GH119 sharing the catalytic machinery with the α-amylase family GH57

FEBS Letters

Volumn 586, Issue 19, 2012, Pages 3360-3366

  Janeček, Štefan ^a,b   Kuchtová, Andrea ^a,b  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

^b UNIVERSITY OF SS CYRIL AND METHODIUS   (Slovakia)

Author keywords

Amylase; Catalytic machinery; Conserved sequence region; Evolutionary relatedness; Family GH119; Family GH57

Indexed keywords

AMYLASE; ASPARTIC ACID; GLUTAMIC ACID; GLYCOSIDASE; NUCLEOPHILE; PROTON;

ARTICLE; BACILLUS CIRCULANS; COMPUTER MODEL; ENZYME ACTIVE SITE; ENZYME STRUCTURE; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALPHA-AMYLASES; AMINO ACID SEQUENCE; BACILLUS; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GLYCOSIDE HYDROLASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

BACILLUS CIRCULANS;

EID: 84866630737     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.07.020     Document Type: Article

References (40)

1. E.A. MacGregor, S. Janecek, and B. Svensson Relationship of sequence and structure to specificity in the α-amylase family of enzymes Biochim. Biophys. Acta 1546 2001 1 20
2. N. Aghajari, M. Roth, and R. Haser Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic α-amylase Biochemistry 41 2002 4273 4280
3. S. Janecek, E.A. MacGregor, and B. Svensson Characteristic differences in the primary structure allow discrimination of cyclodextrin glucanotransferases from α-amylases Biochem. J. 305 1995 685 686
4. B.L. Cantarel, P.M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics Nucleic Acids Res. 37 2009 D233 D238
5. E.A. MacGregor, and B. Svensson A super-secondary structure predicted to be common to several α-1,4-d-glucan-cleaving enzymes Biochem. J. 259 1989 145 152
6. B. Henrissat A classification of glycosyl hydrolases based on amino acid sequence similarities Biochem. J. 280 1991 309 316
7. H. Takata, T. Kuriki, S. Okada, Y. Takesada, M. Iizuka, N. Minamiura, and T. Imanaka Action of neopullulanase. Neopullulanase catalyzes both hydrolysis and transglycosylation at α-(1→4)- and α-(1→6)-glucosidic linkages J. Biol. Chem. 267 1992 18447 18452
8. 8-barrel domain and evolutionary relationship to other amylolytic enzymes J. Protein Chem. 12 1993 791 805
9. S. Janecek Parallel β/α-barrels of α-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of β-amylase: evolutionary distance is a reflection of unrelated sequences FEBS Lett. 353 1994 119 123
10. M.R. Stam, E.G. Danchin, C. Rancurel, P.M. Coutinho, and B. Henrissat Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins Protein Eng. Des. Sel. 19 2006 555 562
11. Y. Matsuura, M. Kusunoki, W. Harada, and M. Kakudo Structure and possible catalytic residues of Taka amylase A J. Biochem. 95 1984 697 702
12. J.C.M. Uitdehaag, R. Mosi, K.H. Kalk, B.A. van der Veen, L. Dijkhuizen, S.G. Withers, and B.W. Dijkstra X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family Nature Struct. Biol. 6 1999 432 436
13. S. Janecek How many conserved sequence regions are there in the α-amylase family? Biologia 57 Suppl. 11 2002 29 41
14. B. Henrissat, and A. Bairoch Updating the sequence-based classification of glycosyl hydrolases Biochem. J. 316 1996 695 696
15. S. Janecek Amylolytic families of glycoside hydrolases: focus on the family GH-57 Biologia 60 Suppl. 16 2005 177 184
16. K. Blesak, and S. Janecek Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57 Extremophiles 16 2012 497 506
17. M. Palomo, T. Pijning, T. Booiman, J.M. Dobruchowska, J. van der Vlist, S. Kralj, A. Planas, K. Loos, J.P. Kamerling, B.W. Dijkstra, M.J. van der Maarel, L. Dijkhuizen, and H. Leemhuis Thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed J. Biol. Chem. 286 2011 3520 3530
18. H. Imamura, S. Fushinobu, M. Yamamoto, T. Kumasaka, B.S. Jeon, T. Wakagi, and H. Matsuzawa Crystal structures of 4-α-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor J. Biol. Chem. 278 2003 19378 19386
19. A. Dickmanns, M. Ballschmiter, W. Liebl, and R. Ficner Structure of the novel α-amylase AmyC from Thermotoga maritima Acta Crystallogr. D Biol. Crystallogr. 62 2006 262 270
20. C.R. Santos, C.C. Tonoli, D.M. Trindade, C. Betzel, H. Takata, T. Kuriki, T. Kanai, T. Imanaka, R.K. Arni, and M.T. Murakami Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 Proteins 79 2011 547 557
21. R. Zona, F. Chang-Pi-Hin, M.J. O'Donohue, and S. Janecek Bioinformatics of the glycoside hydrolase family 57 and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis Eur. J. Biochem. 271 2004 2863 2872
22. S. Janecek, and K. Blesak Sequence-structural features and evolutionary relationships of family GH57 α-amylases and their putative α-amylase-like homologues Protein J. 30 2011 429 435
23. H. Watanabe, T. Nishimoto, M. Kubota, H. Chaen, and S. Fukuda Cloning, sequencing, and expression of the genes encoding an isocyclomaltooligosaccharide glucanotransferase and an α-amylase from a Bacillus circulans strain Biosci. Biotechnol. Biochem. 70 2006 2690 2702
24. D.G. Naumoff Hierarchical classification of glycoside hydrolases Biochemistry (Moscow) 76 2011 622 635
25. D.A. Comfort, C.J. Chou, S.B. Conners, A.L. VanFossen, and R.M. Kelly Functional-genomics-based identification and characterization of open reading frames encoding α-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus Appl. Environ. Microbiol. 74 2008 1281 1283
26. H. Wang, Y. Gong, W. Xie, W. Xiao, J. Wang, Y. Zheng, J. Hu, and Z. Liu Identification and characterization of a novel thermostable gh-57 gene from metagenomic fosmid library of the Juan de Fuca Ridge hydrothemal vent Appl. Biochem. Biotechnol. 164 2011 1323 1338
27. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
28. R. Apweiler, M.J. Martin, C. O'Donovan, M. Magrane, Y. Alam-Faruque, R. Antunes, and D. Barrell The Universal Protein Resource (UniProt) in 2010 Nucleic Acids Res. 38 2010 D142 D148
29. D.A. Benson, I. Karsch-Mizrachi, D.J. Lipman, J. Ostell, and E.W. Sayers GenBank Nucleic Acids Res. 39 2011 D32 D37
30. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, and D.G. Higgins Clustal W and Clustal X version 2.0 Bioinformatics 23 2007 2947 2948
31. N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W. Townsend-Merino, Q. Zhang, C. Knezevich, L. Xie, L. Chen, Z. Feng, R.K. Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Berman, and P.E. Bourne The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema Nucleic Acids Res. 33 2005 D233 D237
32. L.A. Kelley, and M.J.E. Sternberg Protein structure prediction on the Web: a case study using the Phyre server Nat. Protoc. 4 2009 363 371
33. F. Kiefer, K. Arnold, M. Kunzli, L. Bordoli, and T. Schwede The SWISS-MODEL repository and associated resources Nucleic Acids Res. 37 2009 D387 D392
34. M. Shatsky, R. Nussinov, and H.J. Wolfson A method for simultaneous alignment of multiple protein structures Proteins 56 2004 143 156
35. N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
36. R.D. Page TreeView: an application to display phylogenetic trees on personal computers Comput. Appl. Biosci. 12 1996 357 358
37. H. Imamura, S. Fushinobu, B.S. Jeon, T. Wakagi, and H. Matsuzawa Identification of the catalytic residue of Thermococcus litoralis 4-α-glucanotransferase through mechanism-based labeling Biochemistry 40 2001 12400 12406
38. S. Kang, C. Vieille, and J.G. Zeikus Identification of Pyrococcus furiosus amylopullulanase catalytic residues Appl. Microbiol. Biotechnol. 66 2005 408 413
39. S.Y. Tang, S.J. Yang, H. Cha, E.J. Woo, C. Park, and K.H. Park Contribution of W229 to the transglycosylation activity of 4-α- glucanotransferase from Pyrococcus furiosus Biochim. Biophys. Acta 1764 2006 1633 1638
40. G.J. Davies, K.S. Wilson, and B. Henrissat Nomenclature for sugar-binding subsites in glycosyl hydrolases Biochem. J. 321 1997 557 559