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Characterization and implications of Ca2+ binding to pectate lyase C.

Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F
J Biol Chem 278 12271-7 (2003)
Related entries: 1o88, 1o8d, 1o8e, 1o8f, 1o8g, 1o8i, 1o8j, 1o8k, 1o8l, 1o8m

Cited: 21 times
EuropePMC logo PMID: 12540845

Abstract

Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have been solved and refined at a resolution of 2.2 A. The Ca(2+) site represents a new motif for Ca(2+), consisting primarily of beta-turns and beta-strands. The principal differences between PelC and the PelC-Ca(2+) structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK(a) values, the presence of Ca(2+) and associated structural changes lower the pK(a) of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca(2+) affinity for PelC is weak, as the K(d) was estimated to be 0.132 (+/-0.004) mm at pH 9.5, 1.09 (+/-0.29) mm at pH 11.2, and 5.84 (+/-0.41) mm at pH 4.5 from x-ray diffraction studies and 0.133 (+/-0.045) mm at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca(2+) affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca(2+) concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca(2+) ion in PelC has multiple functions.

Reviews citing this publication (2)

  1. Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Garron ML, Cygler M. Glycobiology 20 1547-1573 (2010)
  2. The structures and applications of microbial chondroitin AC lyase. Fan XM, Zhou LJ, Huang JY, Zhang YW. World J Microbiol Biotechnol 38 199 (2022)

Articles citing this publication (19)

  1. The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M. J Biol Chem 279 32882-32896 (2004)
  2. Aspen pectate lyase PtxtPL1-27 mobilizes matrix polysaccharides from woody tissues and improves saccharification yield. Biswal AK, Soeno K, Gandla ML, Immerzeel P, Pattathil S, Lucenius J, Serimaa R, Hahn MG, Moritz T, Jönsson LJ, Israelsson-Nordström M, Mellerowicz EJ. Biotechnol Biofuels 7 11 (2014)
  3. Enzymes with new biochemical properties in the pectinolytic complex produced by Aspergillus niger MIUG 16. Dinu D, Nechifor MT, Stoian G, Costache M, Dinischiotu A. J Biotechnol 131 128-137 (2007)
  4. Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid. Shaya D, Hahn BS, Bjerkan TM, Kim WS, Park NY, Sim JS, Kim YS, Cygler M. Glycobiology 18 270-277 (2008)
  5. Interaction of Ca2+ with uracil and its thio derivatives in the gas phase. Trujillo C, Lamsabhi AM, Mó O, Yáñez M, Salpin JY. Org Biomol Chem 6 3695-3702 (2008)
  6. Crystal structure and substrate-binding mode of a novel pectate lyase from alkaliphilic Bacillus sp. N16-5. Zheng Y, Huang CH, Liu W, Ko TP, Xue Y, Zhou C, Guo RT, Ma Y. Biochem Biophys Res Commun 420 269-274 (2012)
  7. A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller. Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K. J Biol Chem 282 37134-37145 (2007)
  8. Mining Xanthomonas and Streptomyces genomes for new pectinase-encoding sequences and their heterologous expression in Escherichia coli. Xiao Z, Boyd J, Grosse S, Beauchemin M, Coupe E, Lau PC. Appl Microbiol Biotechnol 78 973-981 (2008)
  9. pH-Dependent structural changes at Ca(2+)-binding sites of coagulation factor IX-binding protein. Suzuki N, Fujimoto Z, Morita T, Fukamizu A, Mizuno H. J Mol Biol 353 80-87 (2005)
  10. Characterization and Functional Analysis of the Poplar Pectate Lyase-Like Gene PtPL1-18 Reveal Its Role in the Development of Vascular Tissues. Bai Y, Wu D, Liu F, Li Y, Chen P, Lu M, Zheng B. Front Plant Sci 8 1123 (2017)
  11. Role of pectinolytic enzymes identified in Clostridium thermocellum cellulosome. Chakraborty S, Fernandes VO, Dias FM, Prates JA, Ferreira LM, Fontes CM, Goyal A, Centeno MS. PLoS One 10 e0116787 (2015)
  12. Novel mutants of Erwinia carotovora subsp. carotovora defective in the production of plant cell wall degrading enzymes generated by Mu transpososome-mediated insertion mutagenesis. Laasik E, Ojarand M, Pajunen M, Savilahti H, Mäe A. FEMS Microbiol Lett 243 93-99 (2005)
  13. Potential role of pectate lyase and Ca(2+) in the increase in strawberry fruit firmness induced by short-term treatment with high-pressure CO2. Wang MH, Kim JG, Ahn SE, Lee AY, Bae TM, Kim DR, Hwang YS. J Food Sci 79 S685-92 (2014)
  14. Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming. Zhou Z, Liu Y, Chang Z, Wang H, Leier A, Marquez-Lago TT, Ma Y, Li J, Song J. Appl Microbiol Biotechnol 101 2919-2929 (2017)
  15. Cloning and heterologous expression of a thermostable pectate lyase from Penicillium occitanis in Escherichia coli. Damak N, Abdeljalil S, Koubaa A, Trigui S, Ayadi M, Trigui-Lahiani H, Kallel E, Turki N, Djemal L, Belghith H, Taieb NH, Gargouri A. Int J Biol Macromol 62 549-556 (2013)
  16. Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum. Lara-Márquez A, Oyama K, Zavala-Páramo MG, Villa-Rivera MG, Conejo-Saucedo U, Cano-Camacho H. J Mol Evol 85 120-136 (2017)
  17. 1.37 Å crystal structure of pathogenic factor pectate lyase from Acidovorax citrulli. Tang Q, Liu YP, Ren ZG, Yan XX, Zhang LQ. Proteins 81 1485-1490 (2013)
  18. Improvement on Thermostability of Pectate Lyase and Its Potential Application to Ramie Degumming. Xu H, Feng X, Yang Q, Zheng K, Yi L, Duan S, Cheng L. Polymers (Basel) 14 2878 (2022)
  19. Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming. Zhou C, Cao Y, Xue Y, Liu W, Ju J, Ma Y. Int J Mol Sci 24 538 (2022)


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