The 2 A resolution structure of the sulfate-binding protein involved in active transport in Salmonella typhimurium.
The 2 A resolution structure of the sulfate-binding protein involved in active transport in Salmonella typhimurium.
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图 2 参与鼠伤寒沙门氏菌主动转运的硫酸盐结合蛋白的解析结构。
DOI：
10.1016/0022-2836(88)90341-5
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发表时间：
1988
影响因子：
5.6
通讯作者：
Quiocho,FA
中科院分区：
文献类型：
--
作者：
Pflugrath,JW;Quiocho,FA
硫酸盐结合蛋白的配体形式的晶体结构，一个初始受体的主动运输硫酸盐在鼠伤寒沙门氏菌，已解决和完善，在2.0 μ m分辨率（1 μ m = 0.1 nm）。最终的模型由2422个非氢原子、一个硫酸盐底物和143个水分子组成，在8到2 μ m之间的16，959次反射中产生了14.0%的晶体学R因子。结构偏离理想键长和角距离分别为0.015和0.037 π。该蛋白质为椭圆体，整体尺寸为35 μ m × 35 μ m × 65 μ m，由两个相似的球状结构域组成。这两个结构域由三个不同的肽段连接，这些肽段虽然在氨基酸序列中相距甚远，但在三级结构中非常接近。由于这些连接片段位于分子的周边附近，它们进一步充当两个结构域之间形成的深裂缝的基部或“边界”。尽管结构域间有着不寻常的连接性，但两个结构域都有着相似的超二级结构，由一个中央五股β折叠片层和两侧的α螺旋组成。两个结构域的排列导致了椭圆形形状和两个结构域之间的裂缝，其中发现并完全吞噬了硫酸盐底物。一个相当重要的发现是硫酸盐底物主要通过七个氢键紧紧地固定在适当的位置，其中五个由主链肽NH基团提供，另一个是丝氨酸羟基，最后一个是色氨酸侧链的吲哚NH部分;在硫酸根二价阴离子的货车范德华距离内没有带正电荷的残基，也没有阳离子，也没有水分子。所有与硫酸根相关的主链肽单元依次连接（维生素肽CO基团）到氢键阵列。其中三个由交替的肽单元和氢键组成，两个与组氨酸和精氨酸残基相连，硫酸盐结合蛋白与本实验室已发现的其他四种周质结合蛋白的结构非常相似，它们分别是l-阿拉伯糖、d-半乳糖/d-葡萄糖、亮氨酸/异亮氨酸/缬氨酸和亮氨酸。相似性包括椭圆形和两个球形结构域结构，每个结构域由两侧为α-螺旋的中央β-折叠片层组成。在所有结合蛋白结构中，两个结构域通过三个单独的肽段连接，底物结合位点位于两个结构域之间形成的裂缝中。除了共同的结构特征之外，从几种周质结合蛋白的高度精细结构中出现的最值得注意的发现是，底物尽管在结构上完全不同（例如，丙氨酸、硫酸盐和氨基酸），但主要通过氢键结合。
The crystal structure of the liganded form of the sulfate-binding protein, an initial receptor for active transport of sulfate inSalmonella typhimurium, has been solved and refined at 2.0 Å resolution (1 Å = 0.1 nm). The final model, which consists of 2422 non-hydrogen atoms, one sulfate substrate and 143 water molecules, yields a crystallographicR-factor of 14.0% for 16,959 reflections between 8 and 2 Å. The structure deviates from ideal bond lengths and angle distances by 0.015 Å and 0.037 Å, respectively. The protein is ellipsoid with overall dimensions of 35 Å × 35 Å × 65 Å and consists of two similar globular domains. The two domains are linked by three distinct peptide segments, which though widely separated in the amino acid sequence, are in close proximity in the tertiary structure. As these connecting segments are located near the periphery of the molecule, they further serve as the base or a “boundary” of the deep cleft formed between the two domains. Despite the unusual interdomain connectivity, both domains have similar supersecondary structure consisting of a central five-stranded β-pleated sheet sandwiched by α-helices on either side. The arrangement of the two domains gives rise to the ellipsoidal shape and to the cleft between the two domains wherein the sulfate substrate is found and completely engulfed.A discovery of considerable importance is that the sulfate substrate is tightly held in place primarily by seven hydrogen bonds, five of which are donated by main-chain peptide NH groups, another by a serine hydroxyl and the last by the indole NH moiety of a tryptophan side-chain; there are no positively charged residues, nor cations, nor water molecules within van der Waals' distance to the sulfate dianion. All the main-chain peptide units associated with the sulfate are in turn linked (viathe peptide CO group) to arrays of hydrogen bonds. Three of these arrays are composed of alternating peptide units and hydrogen bonds within the solvent-exposed part of three α-helices and two are linked to a histidine and an arginine residue.The sulfate-binding protein bears strong similarity to the structures of four other periplasmic binding proteins solved in our laboratory which are specific forl-arabinose,d-galactose/d-glucose, leucine/isoleucine/valine and leucine. The similarity includes the ellipsoidal shape and the two globular domain structures, each domain consisting of a central β-pleated sheet flanked by α-helices. In all of the binding protein structures, the two domains are linked by three separate peptide segments and the substrate binding site is located in the cleft formed between the two domains. Besides the common structural features, the most notable finding emerging from the highly refined structures of several periplasmic binding proteins is that substrates, though completely dissimilar in structure (e.g. saccharides, sulfate and amino acids), are bound primarily by hydrogen bonds.