3A01

Crystal structure of Aristaless and Clawless homeodomains bound to DNA

Summary for 3A01

• Entry DOI: 10.2210/pdb3a01/pdb
• Related: 3A02 3A03
• Descriptor: Homeodomain-containing protein, Homeobox protein aristaless, 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)-3', ... (4 entities in total)
• Functional Keywords: homeodomain, protein-dna complex, dna-binding, homeobox, nucleus, developmental protein, gene regulation-dna complex, gene regulation/dna
• Biological source: Drosophila melanogaster (Fruit fly); More
• Cellular location: Nucleus : Q9VD99 Q06453
• Total number of polymer chains: 8
• Total formula weight: 59880.75

Authors

Miyazono, K.,Nagata, K.,Saigo, K.,Kojima, T.,Tanokura, M. (deposition date: 2009-02-28, release date: 2010-03-09, Last modification date: 2023-11-01)

Primary citation

Miyazono, K.,Zhi, Y.,Takamura, Y.,Nagata, K.,Saigo, K.,Kojima, T.,Tanokura, M.
Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless
Embo J., 29:1613-1623, 2010

PubMed 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.

PubMed: 20389279
DOI: 10.1038/emboj.2010.53

Experimental method

X-RAY DIFFRACTION (2.7 Å)