Lundqvist T, Schneider G
Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center.
J Biol Chem. 1989 Apr 25;264(12):7078-83.
The crystal structure of the binary complex of nonactivated ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and a transition state analogue, 2-carboxy-D-arabinitol 1,5-bisphosphate has been determined to 2.6 A resolution with x-ray crystallographic methods. The transition state analogue binds in a rather extended conformation at the active site. The orientation of the transition state analogue within the active site could be determined from the electron density maps. The P1 phosphate group of the analogue binds at a site built up of residues from loops 5 and 6 of the alpha/beta-barrel. The phosphate group interacts with the side chains of the conserved residues Arg-288, His-321, and Ser-368 and with main chain nitrogens from residues Thr-322 and Gly-323. The second phosphate group of the transition state analogue binds at the opposite side of the barrel close to loops 1 and 8. Significant differences for the positions and interactions of the P2 phosphate group with the enzyme are found in the two subunits of the dimer. The different mode of binding for this phosphate group in the two subunits is interpreted as a consequence of different conformations of the polypeptide chain observed in loops 6 and 8. The P2 phosphate group interacts with the sidechains of Lys-166 and Lys-329. Loop 6, which is disordered in the nonactivated, nonliganded enzyme is considerably more ordered in one of the subunits, probably due to the interaction of the side chain of Lys-329 with the P2 phosphate group. Almost all oxygen atoms are hydrogen bonded to groups on the enzyme. The carboxyl group forms hydrogen bonds to the side chain of the conserved Asn-111. The binding of the transition state analogue to the nonactivated enzyme is different from the binding of the analogue to activated spinach ribulose-bisphosphate carboxylase.
采用X射线晶体学方法，已将来自红螺菌的非活化核酮糖-1,5-二磷酸羧化酶/加氧酶与过渡态类似物2-羧基-D-阿拉伯糖醇1,5-二磷酸的二元复合物的晶体结构解析到2.6 Å的分辨率。过渡态类似物以相当伸展的构象结合在活性位点。可从电子密度图确定过渡态类似物在活性位点内的取向。该类似物的P1磷酸基团结合在由α/β桶状结构的环5和环6的残基构成的位点。磷酸基团与保守残基Arg-288、His-321和Ser-368的侧链以及Thr-322和Gly-323残基的主链氮相互作用。过渡态类似物的第二个磷酸基团结合在桶状结构的另一侧，靠近环1和环8。在二聚体的两个亚基中，发现P2磷酸基团与酶的位置和相互作用存在显著差异。该磷酸基团在两个亚基中的不同结合模式被解释为环6和环8中观察到的多肽链不同构象的结果。P2磷酸基团与Lys-166和Lys-329的侧链相互作用。在非活化、未结合配体的酶中无序的环6在其中一个亚基中更加有序，这可能是由于Lys-329的侧链与P2磷酸基团相互作用所致。几乎所有氧原子都与酶上的基团形成氢键。羧基与保守的Asn-111的侧链形成氢键。过渡态类似物与非活化酶的结合不同于该类似物与活化的菠菜核酮糖-二磷酸羧化酶的结合。
