|
A model of rabbit muscle phosphoglucomutase was refined at 2.7-A resolution by
using two heavy atom derivatives for initial phasing and standard refinement
procedures, including molecular replacement averaging about a 2-fold axis and
dynamic simulation: final R-factor, 0.223 (no solvent modeling); RMS deviation
from standard bond lengths and angles, 0.020 A and 3.6 degrees, respectively
(all 8658 nonhydrogen atoms plus 36,953 reflections (F/sigma greater than or
equal to 3) between 8- and 2.7-A resolutions); average of individually refined
atomic B-factors, 40 A2 (all atoms) and 30 A2 (all atoms in domains I-III). An
H-bonding scheme with 538 main chain H-bonds for the two monomers in the
asymmetric unit and probable ligands for six uranyl ions in one heavy atom
derivative is given. The monomer contains 42 strands/helices arranged into four
alpha/beta-domains. Each of the first three domains contains an alpha 3 beta 4
alpha 1 motif, where the topology of beta 4 is 2,1,3,4:[arrows: see text] which
is a topology not encountered in an extensive search among known protein
structures. A spatial similarity is observed between corresponding residues in
the three repetitions of this motif per monomer, but the minimal mutational
distance between spatially corresponding residues is not statistically
significant. The loop between the antiparallel strands in each of these domains
is an important feature of the active site. In domain IV, beta-sheet topology is
2,1,3,4,5,6:[arrows:see text]. Noncovalent domain/domain interactions within the
monomer are greatest between adjacent domains along the polypeptide chain, which
are not substantially interdigitated and can be cleanly disengaged by altering
the phi/psi torsional angles of three uniquely positioned residues in the model.
The observed hierarchy of noncovalent interactions between structural units
within the crystal, based on a semi-empirical paradigm, suggests that
monomer-monomer contacts within the asymmetric unit are formed during growth of
the lattice and provides a rationale for some of the diffraction characteristics
of phosphoglucomutase crystals. An unusually deep crevice involving 58 residues
is formed by the head-to-tail, twisted semicircular arrangement of the four
domains of the monomer that places no atom more than 12 A from the
water-accessible surface. The active site of the enzyme is extensively buried at
the bottom of this crevice, at the approximate confluence of the four domains.
Other features of the active site, including the surrounding helical dipoles,
and the metal-ion binding pocket are described, together with structure/function
comparisons with a number of other enzymes.
|
