2I13

Aart, a six finger zinc finger designed to recognize ANN triplets

Summary for 2I13

• Entry DOI: 10.2210/pdb2i13/pdb
• Descriptor: 5'-D(*CP*AP*GP*AP*TP*GP*TP*AP*GP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*GP*GP*G)-3', 5'-D(*GP*CP*CP*CP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*CP*TP*AP*CP*AP*TP*CP*T)-3', Aart, ... (6 entities in total)
• Functional Keywords: dna binding, zinc finger, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Mus musculus (house mouse); More
• Cellular location: Nucleus: Q07230
• Total number of polymer chains: 6
• Total formula weight: 71077.38

Authors

Horton, N.C.,Segal, D.J.,Bhakta, M.,Crotty, J.W.,Barbas III, C.F. (deposition date: 2006-08-12, release date: 2006-10-03, Last modification date: 2024-02-21)

Primary citation

Segal, D.J.,Crotty, J.W.,Bhakta, M.S.,Barbas, C.F.,Horton, N.C.
Structure of Aart, a Designed Six-finger Zinc Finger Peptide, Bound to DNA.
J.Mol.Biol., 363:405-421, 2006

PubMed Abstract: Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 A structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5'A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.

PubMed: 16963084
DOI: 10.1016/j.jmb.2006.08.016

Experimental method

X-RAY DIFFRACTION (1.96 Å)