Baikalov I, Schröder I, Kaczor-Grzeskowiak M, Cascio D, Gunsalus R P, Dickerson R E
Molecular Biology Institute, University of California, Los Angeles 90095-1570, USA.
Biochemistry. 1998 Mar 17;37(11):3665-76. doi: 10.1021/bi972365a.
The structure of the Escherichia coli response regulator NarL has been solved in a new, monoclinic space group, and compared with the earlier orthorhombic crystal structure. Because the monoclinic crystal has two independent NarL molecules per asymmetric unit, we now have three completely independent snapshots of the NarL molecule: two from the monoclinic form and one from the orthorhombic. Comparison of these three structures shows the following: (a) The pairing of N and C domains of the NarL molecule proposed from the earlier analysis is in fact correct, although the polypeptide chain connecting domains was, and remains, disordered and not completely visible. The new structure exhibits identical relative orientation of N and C domains, and supplies some of the missing residues, leaving a gap of only seven amino acids. (b) Examination of corresponding features in the three independent NarL molecules shows that deformations in structure produced by crystal packing are negligible. (c) The "telephone receiver" model of NarL activation is confirmed. The N domain of NarL blocks the binding of DNA to the C domain that would be expected from the helix-turn-helix structure of the C domain. Hence, binding can only occur after significant displacement of N and C domains. (d) NarL monomers have a strong tendency toward dimerization involving contacts between helixes alpha 1 in the two monomers, and this may have mechanistic significance in DNA binding. Analogous involvement of helix alpha 1 in intermolecular contacts is also found in UhpA and in the CheY/CheZ complex.
大肠杆菌应答调节因子NarL的结构已在一个新的单斜晶系空间群中解析出来，并与早期的正交晶系晶体结构进行了比较。由于单斜晶系晶体每个不对称单元中有两个独立的NarL分子，我们现在有了NarL分子的三个完全独立的结构快照：两个来自单斜晶系形式，一个来自正交晶系。对这三种结构的比较显示如下：(a) 早期分析提出的NarL分子N结构域和C结构域的配对实际上是正确的，尽管连接结构域的多肽链过去是、现在仍然是无序的且不完全可见。新结构展示了N结构域和C结构域相同的相对取向，并补充了一些缺失的残基，仅留下七个氨基酸的缺口。(b) 对三个独立的NarL分子中相应特征的检查表明，晶体堆积产生的结构变形可忽略不计。(c) NarL激活的“电话听筒”模型得到证实。NarL的N结构域阻止DNA与C结构域结合，而根据C结构域的螺旋-转角-螺旋结构预期会发生这种结合。因此，只有在N结构域和C结构域发生显著位移后才能发生结合。(d) NarL单体有强烈的二聚化倾向，涉及两个单体中α1螺旋之间的接触，这可能在DNA结合中具有机制意义。在UhpA以及CheY/CheZ复合物中也发现α1螺旋类似地参与分子间接触。
