1KC6

HincII Bound to Cognate DNA

Summary for 1KC6

• Entry DOI: 10.2210/pdb1kc6/pdb
• Descriptor: 5'-D(P*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*G)-3', TYPE II RESTRICTION ENZYME HINCII, SODIUM ION, ... (4 entities in total)
• Functional Keywords: restriction endonuclease, blunt cutting, protein-dna, indirect readout, dna bending, hydrolase-dna complex, hydrolase/dna
• Biological source: Haemophilus influenzae
• Total number of polymer chains: 8
• Total formula weight: 133983.76

Authors

Horton, N.C.,Dorner, L.F.,Perona, J.J. (deposition date: 2001-11-07, release date: 2001-12-07, Last modification date: 2024-02-07)

Primary citation

Horton, N.C.,Dorner, L.F.,Perona, J.J.
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
Nat.Struct.Biol., 9:42-47, 2002

PubMed Abstract: The crystal structure of the HincII restriction endonuclease-DNA complex shows that degenerate specificity for blunt-ended cleavage at GTPyPuAC sequences arises from indirect readout of conformational preferences at the center pyrimidine-purine step. Protein-induced distortion of the DNA is accomplished by intercalation of glutamine side chains into the major groove on either side of the recognition site, generating bending by either tilt or roll at three distinct loci. The intercalated side chains propagate a concerted shift of all six target-site base pairs toward the minor groove, producing an unusual cross-strand purine stacking at the center pyrimidine-purine step. Comparison of the HincII and EcoRV cocrystal structures suggests that sequence-dependent differences in base-stacking free energies are a crucial underlying factor mediating protein recognition by indirect readout.

PubMed: 11742344
DOI: 10.1038/nsb741

Experimental method

X-RAY DIFFRACTION (2.6 Å)