Summary information and primary citation

PDB-id
3a01; SNAP-derived features in text and JSON formats; DNAproDB
Class
gene regulation-DNA
Method
X-ray (2.7 Å)
Summary
Crystal structure of aristaless and clawless homeodomains bound to DNA
Reference
Miyazono K, Zhi Y, Takamura Y, Nagata K, Saigo K, Kojima T, Tanokura M (2010): "Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless." Embo J., 29, 1613-1623. doi: 10.1038/emboj.2010.53.
Abstract
To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js