Description
Experimental Technique/Method:X-RAY DIFFRACTION
Resolution:1.96
Classification:DNA BINDING PROTEIN/DNA
Release Date:2006-10-03
Deposition Date:2006-08-12
Revision Date:2008-05-01#2011-07-13
Molecular Weight:71077.38
Macromolecule Type:Protein#DNA
Residue Count:468
Atom Site Count:4117
DOI:10.2210/pdb2i13/pdb
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.
Resolution:1.96
Classification:DNA BINDING PROTEIN/DNA
Release Date:2006-10-03
Deposition Date:2006-08-12
Revision Date:2008-05-01#2011-07-13
Molecular Weight:71077.38
Macromolecule Type:Protein#DNA
Residue Count:468
Atom Site Count:4117
DOI:10.2210/pdb2i13/pdb
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.
| Date made available | 2006 |
|---|---|
| Publisher | RCSB-PDB |