title: Crystal structure and functional implications of the tandem-type universal stress protein UspE from Escherichia coli.
abstract: BACKGROUND
  The universal stress proteins (USP) family member UspE is a tandem-type USP that consists of two Usp domains. The UspE expression levels of the Escherichia coli (E. coli) become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. It has been shown that UspA family members are survival factors during cellular growth arrest. The structures and functions of the UspA family members control the growth of E. coli in animal hosts. While several UspA family members have known structures, the structure of E. coli UspE remains to be elucidated.
  
  
  RESULTS
  To understand the biochemical function of UspE, we have determined the crystal structure of E. coli UspE at 3.2 Å resolution. The asymmetric unit contains two protomers related by a non-crystallographic symmetry, and each protomer contains two tandem Usp domains. The crystal structure shows that UspE is folded into a fan-shaped structure similar to that of the tandem-type Usp protein PMI1202 from Proteus mirabilis, and it has a hydrophobic cavity that binds its ligand. Structural analysis revealed that E. coli UspE has two metal ion binding sites, and isothermal titration calorimetry suggested the presence of two Cd(2+) binding sites with a Kd value of 38.3-242.7 μM. Structural analysis suggested that E. coli UspE has two Cd(2+) binding sites (Site I: His117, His 119; Site II: His193, His244).
  
  
  CONCLUSIONS
  The results show that the UspE structure has a hydrophobic pocket. This pocket is strongly bound to an unidentified ligand. Combined with a previous study, the ligand is probably related to an intermediate in lipid A biosynthesis. Subsequently, sequence analysis found that UspE has an ATP binding motif (Gly(269)- X2-Gly(272)-X9-Gly(282)-Asn) in its C-terminal domain, which was confirmed by in vitro ATPase activity monitored using Kinase-Glo® Luminescent Kinase Assay. However, the residues constituting this motif were disordered in the crystal structure, reflecting their intrinsic flexibility. ITC experiments revealed that the UspE probably has two Cd(2+) binding sites. The His117, His 119, His193, and His244 residues within the β-barrel domain are necessary for Cd(2+) binding to UspE protein. As mentioned above, USPs are associated with several functions, such as cadmium binding, ATPase function, and involvement in lipid A biosynthesis by some unknown way.
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. yongbinxu@dlnu.edu.cn.|Laboratory of Biomedical Material Engineering, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China. yongbinxu@dlnu.edu.cn.
authors: Yongbin
authors: Y
authors: Xu
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. 121607511@qq.com.
authors: Jianyun
authors: J
authors: Guo
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. 1830263982@qq.com.
authors: Xiaoling
authors: X
authors: Jin
authors: Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea. kjs1728@nate.com.
authors: Jin-Sik
authors: JS
authors: Kim
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. yingji@dlnu.edu.cn.
authors: Ying
authors: Y
authors: Ji
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. fsd@dlnu.edu.cn.
authors: Shengdi
authors: S
authors: Fan
authors: Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul, 151-742, Republic of Korea. hanc210@snu.ac.kr.
authors: Nam-Chul
authors: NC
authors: Ha
authors: Department of Bioengineering, College of Life Science, Dalian Nationalities University, Dalian, 116600, Liaoning, China. mikyeken@dlnu.edu.cn.
authors: Chun-Shan
authors: CS
authors: Quan
mesh_terms: D002104:Cadmium / Q000737:chemistry; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000502:physiology; D006360:Heat-Shock Proteins / Q000737:chemistry* / Q000502:physiology; D008024:Ligands; D011487:Protein Conformation
chemical_list: D029968:Escherichia coli Proteins; D006360:Heat-Shock Proteins; D008024:Ligands; C000610825:UspE protein, E coli; D002104:Cadmium