Tm. Mcphillips et al., STRUCTURE OF THE R65Q MUTANT OF YEAST 3-PHOSPHOGLYCERATE KINASE COMPLEXED WITH MG-AMP-PNP AND 3-PHOSPHO-D-GLYCERATEFE, Biochemistry, 35(13), 1996, pp. 4118-4127
The structure of a ternary complex of the R65Q mutant of yeast 3-phosp
hoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate (M
g AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-r
ay crystallography to 2.4 Angstrom resolution, The structure was solve
d by single isomorphous replacement, anomalous scattering, and solvent
flattening and has been refined to an R-factor of 0.185, with rms dev
iations from ideal bond distance and angles of 0.009 Angstrom and 1.78
degrees, respectively. PGK consists of two domains, with the 3-PG bou
nd to a ''basic patch'' of residues from the N-terminal domain and the
Mg-AMP-PNP interacting with residues from the C-terminal domain. The
two ligands are separated by similar to 11 Angstrom across the interdo
main cleft, The model of the R65Q mutant of yeast PGK is very similar
to the structures of PGK isolated from horse, pig, and Bacillus stearo
thermophilus (rms deviations between equivalent ex-carbons in the indi
vidual domains < 1.0 Angstrom) but exhibits substantial variations wit
h a previously reported yeast structure (rms deviations between equiva
lent alpha-carbons in the individual domains of 2.9-3.2 Angstrom). The
most significant tertiary structural differences among the yeast R65Q
, equine, porcine, and B. stearothermophilus PGK structures occur in t
he relative orientations of the two domains. However, the relationship
s between the observed conformations of PGK are inconsistent with a ''
hinge-bending'' behavior that would close the interdomain cleft. It is
proposed that the available structural and biochemical data on PGK ma
y indicate that the basic patch primarily represents the site of anion
activation and not the catalytically active binding site for 3-PG.