Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.
Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center.
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DOI：
10.1186/1472-6807-6-27
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发表时间：
2006-12-23
影响因子：
--
通讯作者：
Zhang H
中科院分区：
文献类型：
--
作者：
Saikatendu KS;Zhang X;Kinch L;Leybourne M;Grishin NV;Zhang H
选择由来自金黄色葡萄球菌的SA1388基因编码的蛋白质进行结构测定，以阐明其结构域组织并证实我们早期基于远程同源性的预测，即其包含氮调节PII蛋白样结构域。SA1388被预测含有一个中心的PII样结构域和两个侧翼区域，它们一起属于NIF3样蛋白家族。像SA1388这样的蛋白质仍然是一个研究很少的群体，它们的结构特征可以指导未来的研究，旨在了解它们的功能。用硒反常信号单波长反常色散定相法，对SA 1388晶体的结构进行了2.0nm分辨率的解析。它揭示了一个典型的NIF3样折叠，包含两个结构域，其中一个PII样结构域插入在多肽的中间。NIF3样结构域的N和C末端一半参与二聚化，而PII结构域与对称性相关单体形成三聚体接触。总体而言，SA1388的NIF3样结构域被组织为类似于其同源物E. coli ybgI和来自肺炎链球菌的假定蛋白SP1609。环形的任一侧上的开口部分地被由PII结构域形成的三聚体“盖”覆盖。两个NIF3结构域的连接处具有两个结合在似乎是富含组氨酸的活性位点处的锌离子。一个定义明确的电子密度对应于一个内源性结合的配体的身份不明的观察在接近的金属网站。SA1388是NIF3样蛋白质家族中第三个需要进行结构表征的成员，另外两个也是功能未知的假设蛋白质。SA1388的结构证实了我们先前的预测，即分离两个NIF3结构域的插入结构域采用了PII样折叠，并揭示了蛋白质六聚体的整体加帽环形排列。六个PII样结构域形成两个三聚体“盖”，其在任一侧上覆盖环形的中心腔，并且仅提供小开口以允许小分子受调节地进入封闭室。结合配体的电子密度的存在可能提供重要的线索NIF3样蛋白的可能功能。
The protein encoded by the SA1388 gene from Staphylococcus aureus was chosen for structure determination to elucidate its domain organization and confirm our earlier remote homology based prediction that it housed a nitrogen regulatory PII protein-like domain. SA1388 was predicted to contain a central PII-like domain and two flanking regions, which together belong to the NIF3-like protein family. Proteins like SA1388 remain a poorly studied group and their structural characterization could guide future investigations aimed at understanding their function. The structure of SA1388 has been solved to 2.0Å resolution by single wavelength anomalous dispersion phasing method using selenium anomalous signals. It reveals a canonical NIF3-like fold containing two domains with a PII-like domain inserted in the middle of the polypeptide. The N and C terminal halves of the NIF3-like domains are involved in dimerization, while the PII domain forms trimeric contacts with symmetry related monomers. Overall, the NIF3-like domains of SA1388 are organized as a hexameric toroid similar to its homologs, E. coli ybgI and the hypothetical protein SP1609 from Streptococcus pneumoniae. The openings on either side of the toroid are partially covered by trimeric "lids" formed by the PII domains. The junction of the two NIF3 domains has two zinc ions bound at what appears to be a histidine rich active site. A well-defined electron density corresponding to an endogenously bound ligand of unknown identity is observed in close proximity to the metal site. SA1388 is the third member of the NIF3-like family of proteins to be structurally characterized, the other two also being hypothetical proteins of unknown function. The structure of SA1388 confirms our earlier prediction that the inserted domain that separates the two NIF3 domains adopts a PII-like fold and reveals an overall capped toroidal arrangement for the protein hexamer. The six PII-like domains form two trimeric "lids" that cap the central cavity of the toroid on either side and provide only small openings to allow regulated entry of small molecules into the occluded chamber. The presence of the electron density of the bound ligand may provide important clues on the likely function of NIF3-like proteins.
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大肠杆菌蛋白YBGI的晶体结构，一种带有双核金属位点的环形结构。
影响因子：
--
作者：
Ladner, Jane E;Obmolova, Galina;Teplyakov, Alexey;Howard, Andrew J;Khil, Pavel P;Camerini-Otero, R Daniel;Gilliland, Gary L
通讯作者：
Gilliland, Gary L
影响因子：
4.8
作者：
Cho, Y;Sharma, V;Sacchettini, JC
通讯作者：
Sacchettini, JC
DOI：
10.1073/pnas.68.12.2949
发表时间：
1971-01-01
影响因子：
11.1
作者：
BROWN, MS;SEGAL, A;STADTMAN, ER
通讯作者：
STADTMAN, ER
影响因子：
14.9
作者：
Ginalski, K;Rychlewski, L
通讯作者：
Rychlewski, L
影响因子：
14.9
作者：
Andreeva, A;Howorth, D;Murzin, AG
通讯作者：
Murzin, AG