Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.
Nucleotide-binding flexibility in ultrahigh-resolution structures of the SRP GTPase Ffh.
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DOI：
10.1107/s090744490802444x
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发表时间：
2008-10
期刊：
影响因子：
--
通讯作者：
Freymann DM
中科院分区：
文献类型：
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作者：
Ramirez UD;Focia PJ;Freymann DM
在< 1.24 nm分辨率下的Ffh NG GTdR结构域的晶体结构揭示了多种重叠的核苷酸结合模式。 两种结构的核苷酸结合的NG结构域的Ffh，GTdR亚基的细菌信号识别颗粒（SRP），已被确定在100倍分辨率在类似的晶体形式。一个是GDP绑定，一个是GMPPCP绑定。每个结构的不对称单元包含两个蛋白质单体，每个单体在核苷酸结合构象和占据率方面表现出差异。GDP结合的Ffh NG在一个单体中表现出两种结合构象，而另一个单体中没有，并且GMPPCP结合的蛋白质在一个单体中表现出核苷酸的完全占据，但在另一个单体中仅部分占据。因此，在相同的溶液条件下，每个晶体显示出多种结合状态，这表明即使当核苷酸结合时，其在Ffh NG活性位点中的位置也是动态的。结合核苷酸定位的一些差异可能源于晶体包装环境的差异，已经确定的特定因素包括N和G结构域的相对位置、P环中的小构象变化、活性位点内埋藏的沃茨的位置以及与鸟嘌呤碱基包装的闭合环中的移位。然而，“松散”结合可能具有生物学意义，促进容易的核苷酸交换，并提供了一种机制，用于引发的SRP GT3在其激活之前，在其与SRP受体的复合物。
Crystal structures of the Ffh NG GTPase domain at < 1.24 Å resolution reveal multiple overlapping nucleotide binding modes. Two structures of the nucleotide-bound NG domain of Ffh, the GTPase subunit of the bacterial signal recognition particle (SRP), have been determined at ultrahigh resolution in similar crystal forms. One is GDP-bound and one is GMPPCP-bound. The asymmetric unit of each structure contains two protein monomers, each of which exhibits differences in nucleotide-binding conformation and occupancy. The GDP-bound Ffh NG exhibits two binding conformations in one monomer but not the other and the GMPPCP-bound protein exhibits full occupancy of the nucleotide in one monomer but only partial occupancy in the other. Thus, under the same solution conditions, each crystal reveals multiple binding states that suggest that even when nucleotide is bound its position in the Ffh NG active site is dynamic. Some differences in the positioning of the bound nucleotide may arise from differences in the crystal-packing environment and specific factors that have been identified include the relative positions of the N and G domains, small conformational changes in the P-loop, the positions of waters buried within the active site and shifts in the closing loop that packs against the guanine base. However, ‘loose’ binding may have biological significance in promoting facile nucleotide exchange and providing a mechanism for priming the SRP GTPase prior to its activation in its complex with the SRP receptor.