The three-dimensional structure of pectate lyase E, a plant virulence factor from Erwinia chrysanthemi

Plant Physiology

Volumn 106, Issue 3, 1994, Pages 849-862

  Lietzke, Susan E ^a   Yoder, Marilyn D ^a   Keen, Noel T ^a   Jurnak, Frances ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ERWINIA; ERWINIA CHRYSANTHEMI;

EID: 0028191528     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (51)

1. Baker EN, Hubbard RE (1984) Hydrogen bonding in globular proteins. Prog Biophys Mol Biol 44: 97-179
2. Baumann U, Wu S, Flaherty KM, McKay DB (1993) Three-dimensional structure of the alkaline protease of Pseudomonas aeruginosa: a two-domain protein with a calcium binding parallel β roll motif. EMBO J 12: 3357-3364
3. Bhat TN, Cohen GH (1984) OMITMAP: an electron density map suitable for the examination of errors in a macromolecular model. J Appl Crystallogr 17: 244-248
4. Blundell TL, Johnson LN (1976) Protein Crystallography. Academic Press, New York, pp 373-375
5. Brünger AT (1993a) Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr D49: 24-36
6. Brünger AT (1993b) X-PLOR Manual, Version 3.1. Yale University, New Haven, CT
7. Brünger AT, Kuriyan J, Karplus M (1987) Crystallographic R factor refinement by molecular dynamics. Science 235: 458-460
8. Burley SK, Petsko GA (1985) Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science 229: 23-28
9. Cohen FE (1993) The parallel β helix of pectate lyase c: something to sneeze at. Science 260: 1444-1445
10. Collmer A, Keen NT (1986) The role of pectic enzymes in plant pathogenesis. Annu Rev Phytopathol 24: 383-409
11. Condemine G, Dorel C, Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1992) Some of the out genes involved in the secretion of pectate lyases in Erwinia chrysanthemi are regulated by kdgR. Mol Microbiol 6: 3199-3211
12. Crawford M, Kolattukudy PE (1987) Pectate lyase from Fusarium solani f. sp. pisi: purification, characterization, in vitro translation of the mRNA, and involvement in pathogenicity. Arch Biochem Biophys 258: 196-205
13. Fitzgerald P, Madsen N (1986) Improvement of limit diffraction and useful x-ray lifetime of crystals of glycogen debranching enzyme. J Crystal Growth 76: 600-606
14. He SY, Schoedel C, Chatterjee AK, Collmer A (1991a) Cloned Erwinia chrysanthemi out genes enable Escherichia coli to selectively secrete a diverse family of heterologous proteins to its milieu. Proc Natl Acad Sci USA 88: 1079-1083
15. He SY, Schoedel C, Chatterjee AK, Collmer A (1991b) Extracellular secretion of pectate lyase by the Erwinia chrysanthemi out pathway is dependent upon sec-mediated export across the inner membrane. J Bacteriol 173: 4310-4317
16. Hinton JCD, Sidebotham JM, Gill DR, Salmond GPC (1989) Extracellular and periplasmic isoenzymes of pectate lyase from Erwinia carotovora subspecies carotovora belong to different gene families. Mol Microbiol 3: 1785-1795
17. Hodel A, Kim S-H, Brünger AT (1992) Model bias in macromolecular crystal structures. Acta Crystallogr A48: 851-858
18. Howard AJ, Nielson C, Xuong N-H (1985) Software for a diffractometer with multiwire area detector. Methods Enzymol 114: 452-472
19. Jones TA (1985) Interactive computer graphics: FRODO. Methods Enzymol 115: 157-171
20. Jones TA, Cowan S, Zou J-Y, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A47: 110-119
21. Jones TA, Kjeldgaard M (1993) O: The Manual, Version 5.9.1. Uppsala University, Uppsala, Sweden
22. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22: 2577-2637
23. Keen NT, Tamaki S (1986) Structure of two pectate lyase genes from Erwinia chrysanthemi EC16 and their high-level expression in Escherichia coli. J Bacteriol 168: 595-606
24. Kim C, Mosser V, Keen NT, Jurnak F (1989) Preliminary crystallographic analysis of a plant pathogenic factor: pectate lyase. J Mol Biol 208: 365-367
25. Kotoujansky A (1987) Molecular genetics of pathogenesis by softrot erwinias. Annu Rev Phytopathol 25: 405-430
26. Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946-950
27. Kuster-Van Someren M (1991) Characterization of an Aspergillus niger pectin lyase gene family. PhD dissertation. University of Utrecht, The Netherlands
28. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283-291
29. Leszczynski JF, Rose GD (1986) Loops in globular proteins: a novel category of secondary structure. Science 234: 849-855
30. Lindeberg M, Collmer A (1992) Analysis of eight out genes in a cluster required for pectic enzyme secretion by Erwinia chrysanthemi: sequence comparison with secretion genes form other gramnegative bacteria. J Bacteriol 174: 7385-7397
31. Lüthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356: 83-85
32. Matthews B (1968) Solvent content of protein crystals. J Mol Biol 33: 491-497
33. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992) Stereochemical quality of protein structure coordinates. Proteins Struct Funct Genet 12: 345-364
34. Pickersgill R, Jenkins J, Harris G, Nassar W, Robert-Baudouy J (1994) The structure of Bacillus subtilus pectate lyase in complex with calcium. Nature Struct Biol (in press)
35. Preston JF, Rice JD, Ingram LO, Keen NT (1992) Differential depolymerization mechanisms of pectate lyases secreted by Erwinia chrysanthemi EC16. J Bacteriol 174: 2039-2042
36. Rafnar T, Griffith IJ, Kuo MC, Bond JF, Rogers BL, Klapper DG (1991) Cloning of Amb a I (antigen E), the major family of short ragweed pollen. J Biol Chem 266: 1229-1236
37. Read R (1986) Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr A42: 140-149
38. Ring CS, Kneller DG, Langridge R, Cohen FE (1992) Taxonomy and conformational analysis of loops in proteins. J Mol Biol 224: 685-699
39. Singh J, Thornton JM (1985) The interaction between phenylalanine rings in proteins. FEBS Lett 191: 1-6
40. Sprang SR (1993) On a β-roll. Trends Biochem Sci 18: 313-314
41. Tamaki SJ, Gold S, Robeson M, Manulis S, Keen NT (1988) Structure and organization of the pel genes from Erwinia chrysanthemi EC16. J Bacteriol 170: 3468-3478
42. Ten Eyck L, Weaver LA, Matthews BW (1976) A method of obtaining a stereochemically acceptable protein model which fits a set of atomic coordinates. Acta Crystallogr A32: 349-355
43. Terwilliger TC, Eisenberg DE (1983) Unbiased three dimensional refinement of heavy atom parameters by correlation of origin removed Patterson functions. Acta Crystallogr A39: 813-817
44. Walkinshaw MD, Arnott S (1981) Conformations and interactions of pectins. I. X-ray diffraction analyses of sodium pectate in neutral and acidified forms. J Mol Biol 153: 1055-1073
45. Wang B-C (1985) Resolution of phase ambiguity in macromolecular crystallography. Methods Enzymol 115: 90-112
46. Wilmot CM, Thornton JM (1990) β-Turns and their distortions: a proposed new nomenclature. Protein Eng 3: 479-493
47. Wilson AJC (1942) Determination of absolute from relative x-ray intensity data. Nature 150: 90-112
48. Wing RA, Yamaguchi J, Larabell SK, Ursin VM, McCormick S (1989) Molecular and genetic characterization of two pollen-expressed genes that have sequence similarity to pectate lyases of the plant pathogen Erwinia. Plant Mol Biol 14: 17-28
49. Yang Z, Cramer CL, Lacy GH (1992) Erwinia carotovora subsp. carotovora pectic enzymes: in planta gene activation and roles in soft-rot pathogenesis. Mol Plant Microbe Interact 5: 104-112
50. Yoder MD, Keen NT, Jurnak F (1993a) New domain motif: the structure of pectate lyase c, a secreted plant virulence factor. Science 260: 1503-1507
51. Yoder MD, Lietzke SE, Jurnak F (1993b) Unusual structural features in the parallel β helix in pectate lyases. Structure 1: 241-251