Furanosidase superfamily: Search of homologues

Molecular Biology

Volumn 46, Issue 2, 2012, Pages 322-327

  Naumoff, D G ^a,b  

^a WINOGRADSKY INSTITUTE OF MICROBIOLOGY   (Russian Federation)

^b STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

Author keywords

propeller; CAZy; FURAN families; furanosidase; furanosidase superfamily; gene annotation; glycoside hydrolase; hierarchical protein classification; new protein families; protein evolution; PSI Protein Classifier; PSI BLAST; search of homologues

Indexed keywords

EID: 84859878454     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893312010153     Document Type: Article

References (20)

1. Tatusov R. L., Fedorova N. D., Jackson J. D., et al. 2003. The COG database: An updated version includes eukaryotes. BMC Bioinform. 4, Art. 41.
2. Naumov D. G., Doroshenko V. G. 1998. β-Fructosidases: A new superfamily of glycosyl hydrolases. Mol. Biol. (Moscow). 32, 761-766.
3. Naumoff D. G. 2001. β-Fructosidase superfamily: Homology with some α-L-arabinases and β-D-xylosidases. Prot. Struct. Funct. Genet. 42, 66-76.
4. Naumoff D. G. 2011. Hierarchical classification of glycoside hydrolases. Biochemistry (Moscow). 76, 622-635.
5. Carbohydrate-Active Enzymes server. 2011. http://www. cazy. org/.
6. Naumoff D. G. 1999. Conserved sequence motifs in levansucrases and bifunctional β-xylosidases and α-L-arabinases. FEBS Lett. 448, 177-179.
7. Naumoff D. G., Livshits V. A. 2001. Molecular structure of the Lactobacillus plantarum sucrose utilization locus: Comparison with Pediococcus pentosaceus. Mol. Biol. (Moscow) 35, 15-22.
8. Pons T., Naumoff D. G., Martínez-Fleites C., Hernández L. 2004. Three acidic residues are at the active site of a β-propeller architecture in glycoside hydrolase families 32, 43, 62, and 68. Prot. Struct. Funct. Bioinform. 54, 424-432.
9. Naumoff D. G. 2000. Enzymes of fructan synthesis and degradation: Sequence analysis and classification. Abstr. 4th Int. Fructan Symp. "Fructan 2000." August 16-20, 2000. Arolla, Switzerland, P. 1. 4. http://www. kokkinias. com/fructan/admin/abstracts/pdf/naumoff. pdf.
10. Hashimoto K., Yoshida M., Hasumi K. 2011. Isolation and characterization of CcAbf62A, a GH62 α-L-arabinofuranosidase, from the basidiomycete Coprinopsis cinerea. Biosci. Biotechnol. Biochem. 75, 342-345.
11. Rebuffet E., Groisillier A., Thompson A., Jeudy A., Barbeyron T., Czjzek M., Michel G. 2011. Discovery and structural characterization of a novel glycosidase family of marine origin. Environ. Microbiol. 13, 1253-1270.
12. The Pfam Database. 2011. Pfam 25. 0. http://pfam. sanger. ac. uk/.
13. Murzin A. G., Chandonia J.-M., Andreeva A., Howorth D., Lo Conte L., Ailey B. G., Brenner S. E., Hubbard T. J. P., Chothia C. 2011. Structural classification of proteins. http://scop. mrc-lmb. cam. ac. uk/scop/.
14. Nurizzo D., Turkenburg J. P., Charnock S. J., Roberts S. M., Dodson E. J., McKie V. A., Taylor E. J., Gilbert H. J., Davies G. J. 2002. Cellvibrio japonicus α-L-arabinanase 43A has a novel five-blade β-propeller fold. Nature Struct. Biol. 9, 665-668.
15. Chaudhuri I., Söding J., Lupas A. N. 2008. Evolution of the β-propeller fold. Prot. Struct. Funct. Bioinform. 71, 795-803.
16. Naumoff D. G. 2006. Development of a hierarchical classification of the TIM-barrel type glycoside hydrolases. Proc. Fifth Int. Conf. Bioinform. Genome Regulat. Struct. July 16-22, 2006. Novosibirsk, Russia, vol. 1, pp. 294-298. http://www. bionet. nsc. ru/meeting/bgrsproceedings/papers/2006/BGRS-2006-V1-067. pdf.
17. Naumoff D. G. 2010. GH101 family of glycoside hydrolases: Subfamily structure and evolutionary connections with other families. J. Bioinform. Comput. Biol. 8, 437-451.
18. Naumoff D. G., Stepushchenko O. O. 2011. Endo-α-1, 4-polygalactosaminidases and their homologs: Structure and evolution. Mol. Biol. (Moscow). 45, 647-657.
19. Naumoff D. G. 2011. GHL1-GHL15: New families of hypothetical glycoside hydrolases. Mol. Biol. (Moscow). 45, 983-992.
20. Naumoff D. G., Carreras M. 2009. New program PSI Protein Classifier automatizes the PSI-BLAST results analysis. Mol. Biol. (Moscow). 43, 652-664.