A motif of a microbial starch-binding domain found in human genethonin

Bioinformatics

Volumn 18, Issue 11, 2002, Pages 1534-1537

  Janeček, Štefan ^a  

^a Institute of Molecular Biology Slovak Academy of Sciences   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; AMYLASE; CARBOHYDRATE BINDING PROTEIN; CYCLOMALTODEXTRIN GLUCANOTRANSFERASE; MUSCLE PROTEIN; STARCH; GENX 3414 PROTEIN, HUMAN; GENX-3414 PROTEIN, HUMAN; GLUCAN 1,4 ALPHA GLUCOSIDASE; GLUCOSYLTRANSFERASE; MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS; BACTERIAL STRAIN; CONTROLLED STUDY; GENETIC CONSERVATION; HUMAN; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SKELETAL MUSCLE; STRUCTURE ANALYSIS; ASPERGILLUS NIGER; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

BACILLUS SP.; BACTERIA (MICROORGANISMS); POSIBACTERIA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ASPERGILLUS NIGER; CONSERVED SEQUENCE; DATABASES, PROTEIN; GLUCAN 1,4-ALPHA-GLUCOSIDASE; GLUCOSYLTRANSFERASES; HUMANS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUSCLE PROTEINS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SPECIES SPECIFICITY; STARCH;

EID: 0036855905     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.11.1534     Document Type: Article

References (34)

1. Aleshin,A., Golubev,A., Firsov,L.M. and Honzatko,R.B. (1992) Crystal structure of glucoamylase from Aspergillus awamori var. X100 to Å resolution. J. Biol. Chem., 267, 19291-19298.
2. Altschul,S.F., Stephen,F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D. et al. (2000) InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics, 16, 1145-1150.
4. Ashikari,T., Nakamura,N., Tanaka,Y., Kiuchi,N., Shibano,Y., Tanaka,T., Amachi,T. and Yoshizumi,H. (1986) Rhizopus raw-starch-degrading glucoamylase: its cloning and expression in yeast. Agric. Biol. Chem., 50, 957-964.
5. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
6. Bateman,A., Birney,E., Durbin,R., Eddy,S.R., Howe,K.L. and Sonnhammer,E.L. (2000) The Pfam protein families database. Nucleic Acids Res., 28, 263-266.
7. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
8. Bouju,S., Lignon,M.F., Pietu,G., Le Cunff,M., Leger,J.J., Auffray,C. and Dechesne,C.A. (1998) Molecular cloning and functional expression of a novel human gene encoding two 41-43 kDa skeletal muscle internal membrane proteins. Biochem. J., 335, 549-556.
9. Corpet,F., Servant,F., Gouzy,J. and Kahn,D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res., 28, 267-269.
10. Coutinho,P.M. and Henrissat,B. (1999) Carbohydrate-active enzymes: an integrated database approach. In Gilbert,H.J., Davies,G., Henrissat,B. and Svensson,B. (eds), Recent Advances in Carbohydrate Bioengineering. The Royal Society of Chemistry, Cambridge, pp. 3-12.
11. Dalmia,B.K., Schütte,K. and Nikolov,Z.L. (1995) Domain E of Bacillus macerans cyclodextrin glucanotransferase: an independent starch-binding domain. Biotechnol. Bioeng., 47, 575-584.
12. Giardina,T., Gunning,A.P., Juge,N., Faulds,C.B., Furniss,C.S., Svensson,B., Morris,V.J. and Williamson,G. (2001) Both binding sites of the starch-binding domain of Aspergillus niger glucoamylase are essential for inducing a conformational change in amylose. J. Mol. Biol., 313, 1149-1159.
13. Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis, 18, 2714-2723.
14. Harata,K., Haga,K., Nakamura,A., Aoyagi,M. and Yamane,K. (1996) X-ray structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011. Comparison of two independent molecules at 1.8 Å resolution. Acta Crystallogr., D52, 1136-1145.
15. Henrissat,B. and Davies,G. (1997) Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol., 7, 637-644.
16. Janeček,Š. and Ševčík,J. (1999) The evolution of starch-binding domain. FEBS Lett., 456, 119-125.
17. Kelley,L.A., MacCallum,R.M. and Sternberg,M.J.E. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol., 299, 499-520.
18. Kimura,K., Kataoka,S., Ishii,Y., Takano,T. and Yamane,K. (1987) Nucleotide sequence of the β-cyclodextrin glucanotransferase gene of alkalophilic Bacillus sp. strain 1011 and similarity of its amino acid sequence to those of α-amylases. J. Bacteriol., 169, 4399-4402.
19. Lawson,C.L., van Montfort,R., Strokopytov,B., Rozeboom,H.J., Kalk,K.H., de Vries,G.E., Penninga,D., Dijkhuizen,L. and Dijkstra,B.W. (1994) Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. J. Mol. Biol., 236, 590-600.
20. Matsuura,Y., Kusunoki,M., Harada,W. and Kakudo,M. (1984) Structure and possible catalytic residues of Taka-amylase A. J. Biochem., 95, 697-702.
21. Mikami,B., Hehre,E.J., Sato,M., Katsube,Y., Hirose,M., Morita,Y. and Sacchettini,J.C. (1993) The 2.0 Å resolution structure of soybean β-amylase complexed with α-cyclodextrin. Biochemistry, 32, 6836-6845.
22. Minassian,B.A., Ianzano,L., Meloche,M., Andermann,E., Rouleau,G.A., Delgado-Escueta,A.V. and Scherer,S.W. (2000) Mutation spectrum and predicted function of laforin in Lafora's progressive myoclonus epilepsy. Neurology, 55, 341-346.
23. Ohdan,K., Kuriki,T., Takata,H., Kaneko,H. and Okada,S. (2000) Introduction of raw starch-binding domains into Bacillussubtilis α-amylase by fusion with the starch-binding domain of Bacillus cyclomaltodextrin glucanotransferase. Appl. Environ. Microbiol., 66, 3058-3064.
24. Penninga,D., van der Veen,B.A., Knegtel,R.M., van Hijum,S.A., Rozeboom,H.J., Kalk,K.H., Dijkstra,B.W. and Dijkhuizen,L. (1996) The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J. Biol. Chem., 271, 32777-32784.
25. Rodriguez-Sanoja,R., Morlon-Guyot,J., Jore,J., Pintado,J., Juge,N. and Guyot,J.P. (2000) Comparative characterization of complete and truncated forms of Lactobacillus amylovorus α-amylase and role of the C-terminal direct repeats in raw-starch binding. Appl. Environ. Microbiol., 66, 3350-3356.
26. Sorimachi,K., Le Gal-Coëffet,M.F., Williamson,G., Archer,D.B. and Williamson,M.P. (1997) Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to β-cyclodextrin. Structure, 5, 647-661.
27. Søgaard,M., Kadziola,A., Haser,R. and Svensson,B. (1993) Site-directed mutagenesis of histidine 93, aspartic acid 180, glutamic acid 205, histidine 290, and aspartic acid 291 at the active site and tryptophan 279 at the raw starch binding site in barley α-amylase 1. J. Biol. Chem., 268, 22480-22484.
28. Sumitani,J., Tottori,T., Kawaguchi,T. and Arai,M. (2000) New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 α-amylase contributes to starch binding and raw starch degrading. Biochem. J., 350, 477-484.
29. Svensson,B., Jespersen,H., Sierks,M.R. and MacGregor,E.A. (1989) Sequence homology between putative raw-starch binding domains from different starch-degrading enzymes. Biochem. J., 264, 309-311.
30. Svensson,B., Larsen,K., Svendsen,I. and Boel,E. (1983) The complete amino acid sequence of the glycoprotein, glucoamylase G1, from Aspergillus niger. Carlsberg Res. Commun., 48, 529-544.
31. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment trough sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
32. Tibbot,B.K., Wong,D.W. and Robertson,G.H. (2000) A functional raw starch-binding domain of barley α-amylase expressed in Escherichia coli. J. Protein Chem., 19, 663-669.
33. Uitdehaag,J.C.M., Mosi,R.M., Kalk,K.H., van der Veen,B.A., Dijkhuizen,L., Withers,S.G. and Dijkstra,B.W. (1999) X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family. Nature Struct. Biol., 6, 432-436.
34. Wang,J., Stuckey,J.A., Wishart,M.J. and Dixon,J.E. (2002) A unique carbohydrate binding domain targets the Lafora disease phosphatase to glycogen. J. Biol. Chem., 277, 2377-2380.