The Structural Basis for Exopolygalacturonase Activity in a Family 28 Glycoside Hydrolase

Journal of Molecular Biology

Volumn 368, Issue 5, 2007, Pages 1215-1222

  Abbott, D Wade ^a   Boraston, Alisdair B ^a  

^a UNIVERSITY OF VICTORIA   (Canada)

Author keywords

exopolygalacturonase; glycoside hydrolase; pectin degradation; X ray crystallography; Yersinia enterocolitica

Indexed keywords

GLYCOSIDASE; POLYGALACTURONASE; UNCLASSIFIED DRUG; YEGH28 ENZYME;

ARTICLE; COMPLEX FORMATION; ENZYME ACTIVITY; ENZYME STRUCTURE; GENE SEQUENCE; NONHUMAN; POLYMERIZATION; PRIORITY JOURNAL; STRUCTURE ANALYSIS; YERSINIA ENTEROCOLITICA;

BACTERIA (MICROORGANISMS); YERSINIA ENTEROCOLITICA;

EID: 34247253077     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.02.083     Document Type: Article

References (42)

1. Pickersgill R., Smith D., Worboys K., and Jenkins J. Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. J. Biol. Chem. 273 (1998) 24660-24664
2. Cho S.W., Lee S., and Shin W. The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex. J. Mol. Biol. 311 (2001) 863-878
3. van Pouderoyen G., Snijder H.J., Benen J.A., and Dijkstra B.W. Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. FEBS Letters 554 (2003) 462-466
4. van Santen Y., Benen J.A., Schroter K.H., Kalk K. H., Armand S., Visser J., and Dijkstra B.W. 1.68-Å crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. J. Biol. Chem. 274 (1999) 30474-30480
5. Shimizu T., Nakatsu T., Miyairi K., Okuno T., and Kato H. Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. Biochemistry 41 (2002) 6651-6659
6. Federici L., Caprari C., Mattei B., Savino C., Di Matteo A., De Lorenzo G., et al. Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein). Proc. Natl Acad. Sci. USA 98 (2001) 13425-13430
7. Petersen T.N., Kauppinen S., and Larsen S. The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix. Structure 5 (1997) 533-544
8. Yoder M.D., Lietzke S.E., and Jurnak F. Unusual structural features in the parallel beta-helix in pectate lyases. Structure 1 (1993) 241-251
9. Yoder M.D., Keen N.T., and Jurnak F. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science 260 (1993) 1503-1507
10. Jenkins J., and Pickersgill R. The architecture of parallel beta-helices and related folds. Prog. Biophys. Mol. Biol. 77 (2001) 111-115
11. Jenkins J., Mayans O., and Pickersgill R. Structure and evolution of parallel beta-helix proteins. J. Struct. Biol. 122 (1998) 236-246
12. Hugouvieux-Cotte-Pattat N., Condemine G., Nasser W., and Reverchon S. Regulation of pectinolysis in Erwinia chrysanthemi. Annu. Rev. Microbiol. 50 (1996) 213-257
13. Liao C.H., Revear L., Hotchkiss A., and Savary B. Genetic and biochemical characterization of an exopolygalacturonase and a pectate lyase from Yersinia enterocolitica. Can. J. Microbiol. 45 (1999) 396-403
14. Rodionov D.A., Gelfand M.S., and Hugouvieux-Cotte-Pattat N. Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology 150 (2004) 3571-3590
15. Boraston A.B., Warren R.A., and Kilburn D.G. Glycosylation by Pichia pastoris decreases the affinity of a family 2a carbohydrate-binding module from Cellulomonas fimi: a functional and mutational analysis. Biochem. J. 358 (2001) 423-430
16. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55 (1999) 1718-1725
17. Schneider T.R., and Sheldrick G.M. Substructure solution with SHELXD. Acta Crystallog. sect. D 58 (2002) 1772-1779
18. Evans G., and Bricogne G. Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment. Acta Crystallog. sect. D 58 (2002) 976-991
19. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
20. Cowtan K. Error estimation and bias correction in phase-improvement calculations. Acta Crystallog. sect. D 55 (1999) 1555-1567
21. Perrakis A., Harkiolaki M., Wilson K.S., and Lamzin V.S. ARP/wARP and molecular replacement. Acta Crystallog. sect. D 57 (2001) 1445-1450
22. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
23. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
24. Laskowski R.A., MacArthur M.W., Moss D.S., and Thorton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
25. Vaguine A.A., Richelle J., and Wodak S.J. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallog. sect. D 55 (1999) 191-205
26. Potterton E., Briggs P., Turkenburg M., and Dodson E. A graphical user interface to the CCP4 program suite. Acta Crystallog. sect. D 59 (2003) 1131-1137
27. Brunger A.T. Free R-value - a novel statistical quantity for assessing the accuracy of crystal-structures. Nature 355 (1992) 472-475
28. Skerra A. Engineered protein scaffolds for molecular recognition. J. Mol. Recogn. 13 (2000) 167-187
29. Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
30. Leahy D.J., Aukhil I., and Erickson H.P. 2.0 Å crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region. Cell 84 (1996) 155-164
31. Kataeva I.A., Seidel III R.D., Shah A., West L.T., Li X.L., and Ljungdahl L.G. The fibronectin type 3-like repeat from the Clostridium thermocellum cellobiohydrolase CbhA promotes hydrolysis of cellulose by modifying its surface. Appl. Environ. Microbiol. 68 (2002) 4292-4300
32. He S.Y., and Collmer A. Molecular cloning, nucleotide sequence, and marker exchange mutagenesis of the exo-poly-alpha-D-galacturonosidase-encoding pehX gene of Erwinia chrysanthemi EC16. J. Bacteriol. 172 (1990) 4988-4995
33. Davies G., and Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure 3 (1995) 853-859
34. Varrot A., Schulein M., and Davies G.J. Structural changes of the active site tunnel of Humicola insolens cellobiohydrolase, Cel6A, upon oligosaccharide binding. Biochemistry 38 (1999) 8884-8891
35. Varrot A., Hastrup S., Schulein M., and Davies G.J. Crystal structure of the catalytic core domain of the family 6 cellobiohydrolase II, Cel6A, from Humicola insolens, at 1.92 Å resolution. Biochem. J. 337 (1999) 297-304
36. Rouvinen J., Bergfors T., Teeri T., Knowles J.K., and Jones T.A. Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei. Science 249 (1990) 380-386
37. Schubot F.D., Kataeva I.A., Chang J., Shah A.K., Ljungdahl L.G., Rose J.P., and Wang B.C. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum. Biochemistry 43 (2004) 1163-1170
38. Fushinobu S., Hidaka M., Honda Y., Wakagi T., Shoun H., and Kitaoka M. Structural basis for the specificity of the reducing end xylose-releasing exo-oligoxylanase from Bacillus halodurans C-125. J. Biol. Chem. 280 (2005) 17180-17186
39. Proctor M.R., Taylor E.J., Nurizzo D., Turkenburg J. P., Lloyd R.M., Vardakou M., et al. Tailored catalysts for plant cell-wall degradation: redesigning the exo/endo preference of Cellvibrio japonicus arabinanase 43A. Proc. Natl Acad. Sci. USA 102 (2005) 2697-2702
40. Dias F.M., Vincent F., Pell G., Prates J.A., Centeno M.S., Tailford L.E., et al. Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A. J. Biol. Chem. 279 (2004) 25517-25526
41. Read R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A 42 (1986) 140-149
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