Structure of YraM, a protein essential for growth of Haemophilus influenzae
Structure of YraM, a protein essential for growth of Haemophilus influenzae
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DOI：
10.1002/prot.22033
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发表时间：
2008-10-01
影响因子：
2.9
通讯作者：
Saper, Mark A.
中科院分区：
文献类型：
--
作者：
Vijayalakshmi, J.;Akerley, Brian J.;Saper, Mark A.
不可分型流感嗜血杆菌是一种专性人类寄生虫，经常引起儿童中耳感染，并加剧慢性阻塞性肺病，这是美国第四大死因。目前还没有针对该菌株的有效疫苗。脂蛋白 YraM（基因 HI1655）被确定对于流感嗜血杆菌的生长和生存至关重要，但其功能尚不清楚。序列比较表明YraM是两个蛋白质模块的融合体。我们生长了包含残基 257-573 (YraM-C) 的 YraM 羧基末端模块的晶体，通过多波长异常衍射技术定相衍射数据，并将模型细化至晶体学 R 因子为 0.16（无 R = 0.19），数据分辨率为 1.35 埃。 YraM-C 的轮胎双结构域结构采用与在涉及细菌主动运输的几种周质结合蛋白 (PBP) 的轮胎开放、无配体形式中观察到的折叠类似的折叠方式。来自其他革兰氏阴性物种的 YraM 同源物的序列比对表明，YraM-C 最保守的残基聚集在其他 PBP 结合其同源配体的位置的两个结构域之间。将 YraM-C 建模为类似于 Leu/Ile/Val 结合蛋白 (LIVBP) 的亮氨酸结合形式的闭合构象，显示出比 LIVBP 中亮氨酸结合位点更大的推定结合袋。该口袋具有极性和非极性表面，后者位于亮氨酸侧链与 LIVBP 结合的同一区域。我们讨论了 YraM 可能的生物学功能，考虑到它在外膜中的预测位置，外膜是这种结合蛋白的一个新位置。
Nontypeable Haemophilus influenzae is an obligate human parasite that Often causes middle ear infections in children and exacerbates chronic obstructive pulmonary disorder, the fourth leading cause of death in the United States. There are no effective vaccines available for this strain. The lipoprotein YraM (gene HI1655) was identified as essential for the growth and viability of H. influenzae but its function is unknown. Sequence comparisons showed that YraM is a fusion of two protein modules. We grew crystals of the carboxyl-terminal module of YraM comprising residues 257-573 (YraM-C), phased the diffraction data by the multiwavelength anomalous diffraction technique, and refined the model to a crystallographic R-factor of 0.16 (R-free = 0.19) with data to 1.35 angstrom resolution. Tire two-domain structure of YraM-C adopts a fold similar to that observed for tire open, unliganded forms of several periplasmic binding proteins (PBPs) involved in bacterial active transport. Sequence alignments of YraM homologues from other Gram-negative species showed that the most conserved residues of YraM-C cluster between the two domains in tire location where other PBPs bind their cognate ligand. Modeling of YraM-C into a closed conformation similar to the leucine-bound form of the Leu/Ile/Val-binding protein (LIVBP) shows a putative binding pocket larger than the leucine-binding site in LIVBP. The pocket has both polar and nonpolar surfaces, with the latter located in the same area where a leucine side chain binds to LIVBP. We discuss possible biological functions of YraM considering its predicted location in the outer membrane, a novel place for such a binding protein.