A Novel Glycoside Hydrolase Family 105: The Structure of Family 105 Unsaturated Rhamnogalacturonyl Hydrolase Complexed with a Disaccharide in Comparison with Family 88 Enzyme Complexed with the Disaccharide

Journal of Molecular Biology

Volumn 360, Issue 3, 2006, Pages 573-585

  Itoh, Takafumi ^a   Ochiai, Akihito ^a   Mikami, Bunzo ^a   Hashimoto, Wataru ^a   Murata, Kousaku ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

bacterial enzyme degrading rhamnogalacturonan; glycoside hydrolase family 105; unsaturated rhamnogalacturonyl hydrolase; YesR; YteR

Indexed keywords

GLYCOSIDASE;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; CHEMICAL REACTION; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME DEGRADATION; ESCHERICHIA COLI; GENE SEQUENCE; MOLECULAR DYNAMICS; MUTAGENESIS; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33745670608     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.04.047     Document Type: Article

References (40)

1. Albersheim P., Neukom H., and Stutz E. Pectic substances and pectic enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 20 (1958) 341-382
2. Schols H.A., Vierhuis E., Bakx E.J., and Voragen A.G. Different populations of pectic hairy regions occur in apple cell walls. Carbohydr. Res. 275 (1995) 343-360
3. McNeil M., Darvill A.G., Fry S.C., and Albersheim P. Structure and function of the primary cell walls of plants. Annu. Rev. Biochem. 53 (1984) 625-663
4. O'Neill M.A., Warrenfeltz D., Kates K., Pellerin P., Doco T., Darvill A.G., and Albersheim P. Rhamnogalacturonan-II, a pectic polysaccharide in the walls of growing plant cell, forms a dimer that is covalently cross-linked by a borate ester. In vitro conditions for the formation and hydrolysis of the dimer. J. Biol. Chem. 271 (1996) 22923-22930
5. Salmond G.P.C. Secretion of extracellular virulence factors by plant pathogenetic bacteria. Annu. Rev. Phytopathol. 32 (1994) 181-200
6. Bauer D.W., Bogdanove A.J., Beer S.V., and Collmer A. Erwinia chrysanthemi hrp genes and their involvement in soft rot pathogenesis and elicitation of the hypersensitive response. Mol. Plant Microbe Interact. 7 (1994) 573-581
7. Hugouvieux-Cotte-Pattat N., Condemine G., Nasser W., and Reverchon S. Regulation of pectinolysis in Erwinia chrysanthemi. Annu. Rev. Microbiol. 50 (1996) 213-257
8. Shevchik V.E., Condemine G., Robert-Baudouy J., and Hugouvieux-Cotte-Pattat N. The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937. J. Bacteriol. 181 (1999) 3912-3919
9. Barras F., van Gijsegem F., and Chatterjee A.K. Extracellular enzymes and pathogenesis of soft-rot Erwinia. Annu. Rev. Phytopathol. 32 (1994) 201-234
10. Sawitzky D. Protein-glycosaminoglycan interactions: infectiological aspects. Med. Microbiol. Immunol. (Berl.) 184 (1996) 155-161
11. Boulnois G.J. Pneumococcal proteins and the pathogenesis of disease caused by Streptococcus pneumoniae. J. Gen. Microbiol. 138 (1992) 259
12. Hashimoto W., Kobayashi E., Nankai H., Sato N., Miya T., Kawai S., and Murata K. Unsaturated glucuronyl hydrolase of Bacillus sp. GL1: novel enzyme prerequisite for metabolism of unsaturated oligosaccharides produced by polysaccharide lyases. Arch. Biochem. Biophys. 368 (1999) 367-374
13. Itoh T., Akao S., Hashimoto W., Mikami B., and Murata K. Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 Å resolution. J. Biol. Chem. 279 (2004) 31804-31812
14. Zhang R., Minh T., Lezondra L., Korolev S., Moy S.F., Collart F., and Joachimiak A. 1.6 Å crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins: Struct. Funct. Genet. 60 (2005) 561-565
15. Coutinho P.M., and Henrissat B. Carbohydrate-active enzymes: an integrated database approach. In: Gilbert H.J., Davies G.J., Henrissat B., and Svensson B. (Eds). Recent Advances in Carbohydrate Bioengineering (1999), The Royal Society of Chemistry, Cambridge, UK 3-12
16. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
17. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
18. Hugouvieux-Cotte-Pattat N. The RhaS activator controls the Erwinia chrysanthemi 3937 genes rhiN, rhiT and rhiE involved in rhamnogalacturonan catabolism. Mol. Microbiol. 51 (2004) 1361-1374
19. Pages S., Valette O., Abdou L., Belaich A., and Belaich J.P. A rhamnogalacturonan lyase in the Clostridium cellulolyticum cellulosome. J. Bacteriol. 185 (2003) 4727-4733
20. Molgaard A., Kauppinen S., and Larsen S. Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Struct. Fold. Des. 15 (2000) 373-383
21. Linker A., Meyer K., and Weissmann B. Enzymatic formation of monosaccharides from hyaluronate. J. Biol. Chem. 213 (1955) 237-248
22. Ludwigs U., Elgavish A., Esko J.D., Meezan E., and Rodén L. Reaction of unsaturated uronic acid residues with mercuric salts. Biochem. J. 245 (1987) 795-804
23. Lehmann J., and Schröter E. Reaktionen enolischer zuckerderivate: Teil VIII. Die wirkung von β-d-glucosidase und β-d-galaktosidase auf d-glucal und d-galaktal. Carbohydr. Res. 23 (1972) 359-368
24. Hehre E.J., Genghof D., Sternlight H., and Brewer C. Scope and mechanism of carbohydrase action: stereospecific hydration of d-glucal catalyzed by α- and β-glucosidase. Biochemistry 16 (1977) 1780-1787
25. Hehre E.J., Brewer C.F., Uchiyama T., Schlesselmann P., and Lehmann J. Scope and mechanism of carbohydrase action. Stereospecific hydration of 2,6-anhydro-1-deoxy-d-gluco-hept-1-enitol catalyzed by α- and β-glucosidases and an inverting exo-α-glucanase. Biochemistry 19 (1980) 3557-3564
26. Brockhaus M., and Lehmann J. 2,6-Anhydro-1-diazo-1-deoxy-d-glycero-l-manno-heptitol: a specific blocking agent for the active site of β-galactosidase. FEBS Letters 62 (1977) 154-156
27. Schlesselmann P., Fritz H., Lehmann J., Uchiyama T., Brewer C.F., and Hehre E.J. Factors determining steric course of enzymic glycosylation reactions: glycosyl transfer products formed from 2,6-anhydro-1-deoxy-d-gluco-hept-1-enitol by α-glucosidases and an inverting exo-α-glucanase. Biochemistry 21 (1982) 6606-6614
28. Lehmann J., and Zieger B. The stereochemistry of the addition of glycerol to d-galactal, catalyzed by β-d-galactosidase. Carbohydr. Res. 58 (1977) 73-78
29. Weiser W., Lehmann J., Chiba S., Matsui H., Brewer C.F., and Hehre E.J. Steric course of the hydration of d-gluco-octenitol catalyzed by α-glucosidases and by trehalase. Biochemistry 27 (1988) 2294-2300
30. De Vries R.P., Parenicova L., Hinz S.W., Kester H.C., Beldman G., Benen J.A., and Visser J. The β-1,4-endogalactanase A gene from Aspergillus niger is specifically induced on arabinose and galacturonic acid and plays an important role in the degradation of pectic hairy regions. Eur. J. Biochem. 269 (2002) 4985-4993
31. Sakamoto T., Yamada M., Kawasaki H., and Sakai T. Molecular cloning and nucleotide sequence of an endo-1,5-α-l-arabinase gene from Bacillus subtilis. Eur. J. Biochem. 245 (1997) 708-714
32. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd edit. (1989), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
33. Weissbach A., and Hurwitz J. The formation of 2-keto-3-deoxyheptonic acid in extracts of Escherichia coli B.I. Identification. J. Biol. Chem. 234 (1959) 705-709
34. MacGee J., and Doudoroff M. A new phosphorylated intermediate in glucose oxidation. J. Biol. Chem. 210 (1954) 617-626
35. McKie V.A., Vincken J.P., Voragen A.G., van den Broek L.E., Stimson E., and Gilbert H.J. A new family of rhamnogalacturonan lyases contains an enzyme that binds to cellulose. Biochem. J. 355 (2001) 167-177
36. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
37. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
38. Sheldrick G.M., and Schneider T.R. SHELXL: high-resolution refinement. Methods Enzymol. 277 (1997) 319-343
39. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J. Appl. Crystallog. 24 (1991) 946-950
40. Merrit E.A., and Murphy M.E.P. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallog. sect. D 50 (1994) 869-873