2ACJ

Crystal structure of the B/Z junction containing DNA bound to Z-DNA binding proteins

Summary for 2ACJ

• Entry DOI: 10.2210/pdb2acj/pdb
• Descriptor: 5'-D(*GP*TP*CP*GP*CP*GP*CP*GP*CP*CP*AP*TP*AP*AP*AP*CP*C)-3', 5'-D(*AP*CP*GP*GP*TP*TP*TP*AP*TP*GP*GP*CP*GP*CP*GP*CP*G)-3', Double-stranded RNA-specific adenosine deaminase (3 entities in total)
• Functional Keywords: a b-z juction, protein-dna complex, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm: P55265
• Total number of polymer chains: 6
• Total formula weight: 39678.88

Authors

Ha, S.C.,Lowenhaupt, K.,Rich, A.,Kim, Y.-G.,Kim, K.K. (deposition date: 2005-07-19, release date: 2005-10-25, Last modification date: 2024-03-13)

Primary citation

Ha, S.C.,Lowenhaupt, K.,Rich, A.,Kim, Y.G.,Kim, K.K.
Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.
Nature, 437:1183-1186, 2005

PubMed Abstract: Left-handed Z-DNA is a higher-energy form of the double helix, stabilized by negative supercoiling generated by transcription or unwrapping nucleosomes. Regions near the transcription start site frequently contain sequence motifs favourable for forming Z-DNA, and formation of Z-DNA near the promoter region stimulates transcription. Z-DNA is also stabilized by specific protein binding; several proteins have been identified with low nanomolar binding constants. Z-DNA occurs in a dynamic state, forming as a result of physiological processes then relaxing to the right-handed B-DNA. Each time a DNA segment turns into Z-DNA, two B-Z junctions form. These have been examined extensively, but their structure was unknown. Here we describe the structure of a B-Z junction as revealed by X-ray crystallography at 2.6 A resolution. A 15-base-pair segment of DNA is stabilized at one end in the Z conformation by Z-DNA binding proteins, while the other end remains B-DNA. Continuous stacking of bases between B-DNA and Z-DNA segments is found, with the breaking of one base pair at the junction and extrusion of the bases on each side (Fig. 1). These extruded bases may be sites for DNA modification.

PubMed: 16237447
DOI: 10.1038/nature04088

Experimental method

X-RAY DIFFRACTION (2.6 Å)