3C25

Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA

Replaces:  3BVR

Summary for 3C25

• Entry DOI: 10.2210/pdb3c25/pdb
• Related: 3BVQ
• Descriptor: DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3'), DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3'), NotI restriction endonuclease, ... (6 entities in total)
• Functional Keywords: protein-dna complex, restriction enzyme fold, pd-(d/e)-xk, restriction endonuclease, rare-cutting, fe-cys4 motif, iron-sulfur protein, hydrolase-dna complex, hydrolase/dna
• Biological source: Nocardia otitidiscaviarum; More
• Total number of polymer chains: 4
• Total formula weight: 98729.41

Authors

Lambert, A.R.,Sussman, D.,Shen, B.,Stoddard, B.L. (deposition date: 2008-01-24, release date: 2008-02-12, Last modification date: 2024-02-21)

Primary citation

Lambert, A.R.,Sussman, D.,Shen, B.,Maunus, R.,Nix, J.,Samuelson, J.,Xu, S.Y.,Stoddard, B.L.
Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Structure, 16:558-569, 2008

PubMed Abstract: The structure of the rare-cutting restriction endonuclease NotI, which recognizes the 8 bp target 5'-GCGGCCGC-3', has been solved with and without bound DNA. Because of its specificity (recognizing a site that occurs once per 65 kb), NotI is used to generate large genomic fragments and to map DNA methylation status. NotI contains a unique metal binding fold, found in a variety of putative endonucleases, occupied by an iron atom coordinated within a tetrahedral Cys4 motif. This domain positions nearby protein elements for DNA recognition, and serves a structural role. While recognition of the central six base pairs of the target is accomplished via a saturated hydrogen bond network typical of restriction enzymes, the most peripheral base pairs are engaged in a single direct contact in the major groove, reflecting reduced pressure to recognize those positions. NotI may represent an evolutionary intermediate between mobile endonucleases (which recognize longer target sites) and canonical restriction endonucleases.

PubMed: 18400177
DOI: 10.1016/j.str.2008.01.017

Experimental method

X-RAY DIFFRACTION (2.5 Å)