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. 1996 May;111(1):73–92. doi: 10.1104/pp.111.1.73

The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.

S E Lietzke 1, R D Scavetta 1, M D Yoder 1, F Jurnak 1
PMCID: PMC157814  PMID: 12226275

Abstract

The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics techniques to a resolution of 2.2 A and an R factor (an agreement factor between observed structure factor amplitudes) of 16.1%. The final model consists of all 355 amino acids and 157 water molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum ion, which inhibits the enzymatic activity, has also been refined and compared to the metal-free protein. In addition, the structures of pectate lyase C (PelC) in the presence and absence of a lutetium ion have been refined further using an improved algorithm for identifying waters and other solvent molecules. The two putative active site regions of PelE have been compared to those in the refined structure of PelC. The analysis of the atomic details of PelE and PelC in the presence and absence of lanthanide ions provides insight into the enzymatic mechanism of pectate lyases.

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Selected References

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  1. Baker E. N., Hubbard R. E. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol. 1984;44(2):97–179. doi: 10.1016/0079-6107(84)90007-5. [DOI] [PubMed] [Google Scholar]
  2. Barras F., Thurn K. K., Chatterjee A. K. Resolution of four pectate lyase structural genes of Erwinia chrysanthemi (EC16) and characterization of the enzymes produced in Escherichia coli. Mol Gen Genet. 1987 Sep;209(2):319–325. doi: 10.1007/BF00329660. [DOI] [PubMed] [Google Scholar]
  3. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  4. Brünger A. T. Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr D Biol Crystallogr. 1993 Jan 1;49(Pt 1):24–36. doi: 10.1107/S0907444992007352. [DOI] [PubMed] [Google Scholar]
  5. Budelier K. A., Smith A. G., Gasser C. S. Regulation of a stylar transmitting tissue-specific gene in wild-type and transgenic tomato and tobacco. Mol Gen Genet. 1990 Nov;224(2):183–192. doi: 10.1007/BF00271551. [DOI] [PubMed] [Google Scholar]
  6. Colman P. M., Weaver L. H., Matthews B. W. Rare earths as isomorphous calcium replacements for protein crystallography. Biochem Biophys Res Commun. 1972 Mar 24;46(6):1999–2005. doi: 10.1016/0006-291x(72)90750-4. [DOI] [PubMed] [Google Scholar]
  7. González-Candelas L., Kolattukudy P. E. Isolation and analysis of a novel inducible pectate lyase gene from the phytopathogenic fungus Fusarium solani f. sp. pisi (Nectria haematococca, mating population VI). J Bacteriol. 1992 Oct;174(20):6343–6349. doi: 10.1128/jb.174.20.6343-6349.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gysler C., Harmsen J. A., Kester H. C., Visser J., Heim J. Isolation and structure of the pectin lyase D-encoding gene from Aspergillus niger. Gene. 1990 Apr 30;89(1):101–108. doi: 10.1016/0378-1119(90)90211-9. [DOI] [PubMed] [Google Scholar]
  9. Hardman K. D., Ainsworth C. F. Structure of concanavalin A at 2.4-A resolution. Biochemistry. 1972 Dec 19;11(26):4910–4919. doi: 10.1021/bi00776a006. [DOI] [PubMed] [Google Scholar]
  10. Heffron S., Henrissat B., Yoder M. D., Lietzke S., Jurnak F. Structure-based multiple alignment of extracellular pectate lyase sequences. Mol Plant Microbe Interact. 1995 Mar-Apr;8(2):331–334. doi: 10.1094/mpmi-8-0331. [DOI] [PubMed] [Google Scholar]
  11. Henrissat B., Heffron S. E., Yoder M. D., Lietzke S. E., Jurnak F. Functional implications of structure-based sequence alignment of proteins in the extracellular pectate lyase superfamily. Plant Physiol. 1995 Mar;107(3):963–976. doi: 10.1104/pp.107.3.963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hinton J. C., Sidebotham J. M., Gill D. R., Salmond G. P. Extracellular and periplasmic isoenzymes of pectate lyase from Erwinia carotovora subspecies carotovora belong to different gene families. Mol Microbiol. 1989 Dec;3(12):1785–1795. doi: 10.1111/j.1365-2958.1989.tb00164.x. [DOI] [PubMed] [Google Scholar]
  13. Hugouvieux-Cotte-Pattat N., Robert-Baudouy J. Analysis of the regulation of the pelBC genes in Erwinia chrysanthemi 3937. Mol Microbiol. 1992 Aug;6(16):2363–2376. doi: 10.1111/j.1365-2958.1992.tb01411.x. [DOI] [PubMed] [Google Scholar]
  14. Janin J., Wodak S. Conformation of amino acid side-chains in proteins. J Mol Biol. 1978 Nov 5;125(3):357–386. doi: 10.1016/0022-2836(78)90408-4. [DOI] [PubMed] [Google Scholar]
  15. Jones T. A. Diffraction methods for biological macromolecules. Interactive computer graphics: FRODO. Methods Enzymol. 1985;115:157–171. doi: 10.1016/0076-6879(85)15014-7. [DOI] [PubMed] [Google Scholar]
  16. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  17. Keen N. T., Dahlbeck D., Staskawicz B., Belser W. Molecular cloning of pectate lyase genes from Erwinia chrysanthemi and their expression in Escherichia coli. J Bacteriol. 1984 Sep;159(3):825–831. doi: 10.1128/jb.159.3.825-831.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kim C. Y., Mosser V., Keen N., Jurnak F. Preliminary crystallographic analysis of a plant pathogenic factor: pectate lyase. J Mol Biol. 1989 Jul 20;208(2):365–367. doi: 10.1016/0022-2836(89)90397-5. [DOI] [PubMed] [Google Scholar]
  19. Kusters-van Someren M., Flipphi M., de Graaff L., van den Broeck H., Kester H., Hinnen A., Visser J. Characterization of the Aspergillus niger pelB gene: structure and regulation of expression. Mol Gen Genet. 1992 Jul;234(1):113–120. doi: 10.1007/BF00272352. [DOI] [PubMed] [Google Scholar]
  20. Leszczynski J. F., Rose G. D. Loops in globular proteins: a novel category of secondary structure. Science. 1986 Nov 14;234(4778):849–855. doi: 10.1126/science.3775366. [DOI] [PubMed] [Google Scholar]
  21. Lietzke S. E., Yoder M. D., Keen N. T., Jurnak F. The Three-Dimensional Structure of Pectate Lyase E, a Plant Virulence Factor from Erwinia chrysanthemi. Plant Physiol. 1994 Nov;106(3):849–862. doi: 10.1104/pp.106.3.849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Ponder J. W., Richards F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol. 1987 Feb 20;193(4):775–791. doi: 10.1016/0022-2836(87)90358-5. [DOI] [PubMed] [Google Scholar]
  23. Preston J. F., 3rd, Rice J. D., Ingram L. O., Keen N. T. Differential depolymerization mechanisms of pectate lyases secreted by Erwinia chrysanthemi EC16. J Bacteriol. 1992 Mar;174(6):2039–2042. doi: 10.1128/jb.174.6.2039-2042.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. RAMACHANDRAN G. N., RAMAKRISHNAN C., SASISEKHARAN V. Stereochemistry of polypeptide chain configurations. J Mol Biol. 1963 Jul;7:95–99. doi: 10.1016/s0022-2836(63)80023-6. [DOI] [PubMed] [Google Scholar]
  25. Rafnar T., Griffith I. J., Kuo M. C., Bond J. F., Rogers B. L., Klapper D. G. Cloning of Amb a I (antigen E), the major allergen family of short ragweed pollen. J Biol Chem. 1991 Jan 15;266(2):1229–1236. [PubMed] [Google Scholar]
  26. Rogers H. J., Harvey A., Lonsdale D. M. Isolation and characterization of a tobacco gene with homology to pectate lyase which is specifically expressed during microsporogenesis. Plant Mol Biol. 1992 Nov;20(3):493–502. doi: 10.1007/BF00040608. [DOI] [PubMed] [Google Scholar]
  27. Tamaki S. J., Gold S., Robeson M., Manulis S., Keen N. T. Structure and organization of the pel genes from Erwinia chrysanthemi EC16. J Bacteriol. 1988 Aug;170(8):3468–3478. doi: 10.1128/jb.170.8.3468-3478.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Walkinshaw M. D., Arnott S. Conformation and interactions of pectins. I. X-ray diffraction analyses of sodium pectate in neutral and acidified forms. J Mol Biol. 1981 Dec 25;153(4):1055–1073. doi: 10.1016/0022-2836(81)90467-8. [DOI] [PubMed] [Google Scholar]
  29. Weis W. I., Drickamer K., Hendrickson W. A. Structure of a C-type mannose-binding protein complexed with an oligosaccharide. Nature. 1992 Nov 12;360(6400):127–134. doi: 10.1038/360127a0. [DOI] [PubMed] [Google Scholar]
  30. Wilmot C. M., Thornton J. M. Beta-turns and their distortions: a proposed new nomenclature. Protein Eng. 1990 May;3(6):479–493. doi: 10.1093/protein/3.6.479. [DOI] [PubMed] [Google Scholar]
  31. Yoder M. D., Jurnak F. The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism). Plant Physiol. 1995 Feb;107(2):349–364. doi: 10.1104/pp.107.2.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yoder M. D., Keen N. T., Jurnak F. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science. 1993 Jun 4;260(5113):1503–1507. doi: 10.1126/science.8502994. [DOI] [PubMed] [Google Scholar]
  33. Zucker M., Hankin L. Regulation of pectate lyase synthesis in Pseudomonas fluorescens and Erwinia carotovora. J Bacteriol. 1970 Oct;104(1):13–18. doi: 10.1128/jb.104.1.13-18.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]

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