Solution structure of the free Zα domain of human DLM-1 (ZBP1/DAI), a Z-DNA binding domain
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The protein DLM-1 (also called Z-DNA binding protein 1, ZBP1) is the product of the dlm-1 gene. The dlm-1 gene was initially isolated and identified using the RNA differential display technique where they found that it was highly up-regulated in the peritoneal lining tissue of mice bearing nearby ovarian tumors and in activated macrophages (Fu et al. 1999). DLM-1 was proposed to play a role in host defense against tumors, although its precise function was unknown (Fu et al. 1999). In 2001, the N-terminal domain of mouse DLM-1 (ZαDLM-1) was co-crystallized with left-handed Z-DNA (PDB ID 1J75) (Schwartz et al. 2001). The complex structure revealed that ZαDLM-1 is structurally similar to the Zα domain of double-stranded RNA adenosine deaminase ADAR1 (ZαADAR1), the first crystal structure of a protein bound to left-handed Z-DNA (PDB ID 1QBJ) (Schwartz et al. 1999), although they only share about 35 % amino acid sequence identity (Schade et al. 1999; Schwartz et al. 1999)...
KeywordsResidual Dipolar Coupling Phosphodiester Backbone Dihedral Angle Restraint NOESY Peak List Hydrogen Bond Restraint
This work was supported by the National Institute of General Medical Sciences; Protein Structure Initiative-Biology Program; Grant Numbers: U54-GM074958 and U54-GM094597. We thank K. Hamilton, E. Kohan, D. Wang, and T. Acton at the Rutgers’ protein production facility for technical support. All NMR data collection, except RDCs collected at the University of Georgia, was conducted at the Ohio Biomedicine Center of Excellence for Structural Biology and Metabonomics at Miami University.
- Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GV, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Robotic cloning and protein production platform of the Northeast Structural Genomics Consortium. Methods Enzymol 394:210–243CrossRefGoogle Scholar
- Acton TB, Xiao R, Anderson S, Aramini J, Buchwald WA, Ciccosanti C, Conover K, Everett J, Hamilton K, Huang YJ, Janjua H, Kornhaber G, Lau J, Lee DY, Liu G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GV, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT (2011) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 493:21–60CrossRefGoogle Scholar
- Guntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378Google Scholar
- Kahmann JD, Wecking DA, Putter V, Lowenhaupt K, Kim YG, Schmieder P, Oschkinat H, Rich A, Schade M (2004) The solution structure of the N-terminal domain of E3L shows a tyrosine conformation that may explain its reduced affinity to Z-DNA in vitro. Proc Natl Acad Sci USA 101:2712–2717CrossRefADSGoogle Scholar
- Kim K, Khayrutdinov BI, Lee CK, Cheong HK, Kang SW, Park H, Lee S, Kim YG, Jee J, Rich A, Kim KK, Jeon YH (2011) Solution structure of the Z beta domain of human DNA-dependent activator of IFN-regulatory factors and its binding modes to B- and Z-DNAs. Proc Natl Acad Sci USA 108:6921–6926CrossRefADSGoogle Scholar
- Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28:7510–7516CrossRefGoogle Scholar