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PDBsum entry 1o8h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Characterization and implications of ca2+ binding to pectate lyase c.
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Authors
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S.R.Herron,
R.D.Scavetta,
M.Garrett,
M.Legner,
F.Jurnak.
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Ref.
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J Biol Chem, 2003,
278,
12271-12277.
[DOI no: ]
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PubMed id
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Abstract
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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.
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Figure 1.
Fig. 1. Plot of the slow exchange of the solution bathing
PelC crystals. The concentrations of ammonium sulfate (  ) and
polyethylene glycol 8000 (  ) in the
1-ml drop containing a PelC crystal are plotted as a function of
time.
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Figure 6.
Fig. 6. Stereoviews of three types of Ca^2+ binding
motifs. A, the Ca^2+ region of  -lactalbumin
exemplifies the continuous helix-loop-helix Ca^2+ binding motif,
which is associated with tight binding. B, the Ca^2+ region of
phospholipase A2 typifies the discontinuous helix-loop-helix
Ca^2+ binding motif. C, the  -turn/ -strand
Ca^2+ binding motif of PelC exhibits weak binding affinity. In
all figures, the polypeptide backbone of the protein is
represented as a green ribbon, the Ca^2+ ions as yellow spheres,
the oxygen atoms as red rods, and a disulfide bridge as a yellow
bar.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2003,
278,
12271-12277)
copyright 2003.
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