Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium binding.
K.Harata,
T.Akiba.
ABSTRACT
A triclinic crystal of hen egg-white lysozyme obtained from a D2O solution at
313 K was transformed into a new triclinic crystal by slow release of solvent
under a temperature-regulated nitrogen-gas stream. The progress of the
transition was monitored by X-ray diffraction. The transition started with the
appearance of strong diffuse streaks. The diffraction spots gradually fused and
faded with the emergence of diffraction from the new lattice; the scattering
power of the crystal fell to a resolution of 1.5 A from the initial 0.9 A
resolution. At the end of the transition, the diffuse streaks disappeared and
the scattering power recovered to 1.1 A resolution. The transformed crystal
contained two independent molecules and the solvent content had decreased to 18%
from the 32% solvent content of the native crystal. The structure was determined
at 1.1 A resolution and compared with the native structure refined at the same
resolution. The backbone structures of the two molecules in the transformed
crystal were superimposed on the native structure with root-mean-square
deviations of 0.71 and 0.96 A. A prominent structural difference was observed in
the loop region of residues Ser60-Leu75. In the native crystal, a water molecule
located at the centre of this helical loop forms hydrogen bonds to main-chain
peptide groups. In the transformed crystal, this water molecule is replaced by a
sodium ion with octahedral coordination that involves water molecules and a
nitrate ion. The peptide group connecting Arg73 and Asn74 is rotated by 180
degrees so that the CO group of Arg73 can coordinate to the sodium ion. The
change in the X-ray diffraction pattern during the phase transition suggests
that the transition proceeds at the microcrystal level. A mechanism is proposed
for the crystal transformation.
Selected figure(s)
Figure 2.
Figure 2 Crystal packing of the native crystal (a) and the
transformed crystal (b). The structures are viewed along the a
axis. The independent molecules in the asymmetric unit are shown
in a red colour. The transformed crystal contains two molecules
in the unit cell.
Figure 5.
Figure 5 Structure of the sodium-binding site in the native
crystal (a) and the transformed crystal (b). The water molecule
in the native crystal is replaced by a sodium ion in the
transformed crystal. In molecule 1 a nitrate anion is directly
coordinated, but in molecule 2 a nitrate ion is bound by
water-mediated hydrogen bonds.
The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2004,
60,
630-637)
copyright 2004.
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