Okamura H, Hanaoka S, Nagadoi A, Makino K, Nishimura Y
Graduate School of Integrated Science, Yokohama City University, 22-2 Seto, Yokohama, Kanazawa-ku, 236-0027, Japan.
J Mol Biol. 2000 Feb 4;295(5):1225-36. doi: 10.1006/jmbi.1999.3379.
PhoB is a transcriptional activator that binds to the phosphate box in the promoters of the phosphate genes of Escherichia coli. PhoB contains two functional domains, an N-terminal phosphorylation domain and a C-terminal DNA-binding/transactivation domain. Here, the three-dimensional structure of the DNA-binding/transactivation domain has been determined by NMR. It consists of an N-terminal four-stranded beta-sheet, a central three helical bundle and a C-terminal beta-hairpin. The second and third helices form a helix-turn-helix (HTH) variant containing a longer turn than the corresponding turn of the classical HTH motif. The overall architecture is very close to that of the OmpR DNA-binding/transactivation domain, however, the conformation of the long turn region of PhoB, a putative interaction site for the RNA polymerase sigma subunit, is entirely different from that of the corresponding turn of OmpR, which interacts with the alpha subunit. In addition, the third helix of PhoB is three amino acid residues longer than the corresponding helix of OmpR. The binding site of PhoB is a TGTCA sequence and the phospahte box contains the two binding sites. NMR studies of the complexes of the PhoB DNA-binding/transactivation domain bound to several different DNA molecules have revealed that two PhoB molecules bind in a tandem array on the phosphate box. In each complex of PhoB the third helix of the DNA-binding/transactivation domain is likely to recognize the TGTCA sequence from the major groove of DNA and the C-terminal beta-hairpin contacts on the minor groove of the 3' site out of the TGTCA sequence in a non-specific manner. The long turn region facing outward is likely to interact with the sigma subunit.
PhoB是一种转录激活因子，它与大肠杆菌磷酸盐基因启动子中的磷酸盐盒结合。PhoB包含两个功能结构域，一个N端磷酸化结构域和一个C端DNA结合/反式激活结构域。在此，DNA结合/反式激活结构域的三维结构已通过核磁共振确定。它由一个N端四链β折叠、一个中央三螺旋束和一个C端β发夹组成。第二和第三螺旋形成一个螺旋-转角-螺旋（HTH）变体，其转角比经典HTH基序的相应转角更长。整体结构与OmpR DNA结合/反式激活结构域非常相似，然而，PhoB长转角区域的构象，即RNA聚合酶σ亚基的一个假定相互作用位点，与与α亚基相互作用的OmpR相应转角的构象完全不同。此外，PhoB的第三螺旋比OmpR的相应螺旋长三个氨基酸残基。PhoB的结合位点是一个TGTCA序列，磷酸盐盒包含两个结合位点。对与几种不同DNA分子结合的PhoB DNA结合/反式激活结构域复合物的核磁共振研究表明，两个PhoB分子以串联阵列的形式结合在磷酸盐盒上。在PhoB的每个复合物中，DNA结合/反式激活结构域的第三螺旋可能从DNA的大沟中识别TGTCA序列，而C端β发夹以非特异性方式与TGTCA序列3'位点的小沟接触。向外的长转角区域可能与σ亚基相互作用。
