Characterization and implications of Ca2+ binding to pectate lyase C

J Biol Chem. 2003 Apr 4;278(14):12271-7. doi: 10.1074/jbc.M209306200. Epub 2003 Jan 22.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Calcium / metabolism*
  • Crystallography, X-Ray
  • Dickeya chrysanthemi / metabolism*
  • Hydrogen-Ion Concentration
  • Isoenzymes / chemistry*
  • Isoenzymes / metabolism*
  • Polysaccharide-Lyases / chemistry*
  • Polysaccharide-Lyases / metabolism*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary


  • Isoenzymes
  • Polysaccharide-Lyases
  • pectate lyase
  • Calcium

Associated data

  • PDB/1O88
  • PDB/1O8D
  • PDB/1O8E
  • PDB/1O8F
  • PDB/1O8G
  • PDB/1O8H
  • PDB/1O8I
  • PDB/1O8J
  • PDB/1O8K
  • PDB/1O8L
  • PDB/1O8M