3F21

Crystal structure of Zalpha in complex with d(CACGTG)

Summary for 3F21

• Entry DOI: 10.2210/pdb3f21/pdb
• Related: 3F22 3F23
• Descriptor: Double-stranded RNA-specific adenosine deaminase, DNA (5'-D(*DTP*DCP*DAP*DCP*DGP*DTP*DG)-3') (3 entities in total)
• Functional Keywords: protein-z-dna complex, alternative promoter usage, alternative splicing, cytoplasm, disease mutation, dna-binding, hydrolase, metal-binding, mrna processing, nucleus, phosphoprotein, polymorphism, rna-binding, rna-mediated gene silencing, ubl conjugation, zinc
• Biological source: Homo sapiens (Human); More
• Cellular location: Cytoplasm: P55265
• Total number of polymer chains: 6
• Total formula weight: 33347.11

Authors

Ha, S.C.,Choi, J.,Kim, K.K. (deposition date: 2008-10-28, release date: 2008-12-30, Last modification date: 2023-11-08)

Primary citation

Ha, S.C.,Choi, J.,Hwang, H.Y.,Rich, A.,Kim, Y.G.,Kim, K.K.
The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ{alpha}ADAR1
Nucleic Acids Res., 37:629-637, 2009

PubMed Abstract: The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.

PubMed: 19074195
DOI: 10.1093/nar/gkn976

Experimental method

X-RAY DIFFRACTION (2.2 Å)