2FKC

Crystal Form I of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ion

Summary for 2FKC

• Entry DOI: 10.2210/pdb2fkc/pdb
• Related: 1YNM 2FKH 2FL3 2FLC
• Descriptor: 5'-D(*CP*CP*AP*GP*CP*GP*CP*TP*GP*G)-3', R.HinP1I restriction endonuclease, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: restriction endonuclease, protein dimerizaton, dna superhelix, protein-dna-metal ion complex, hydrolase-dna complex, hydrolase/dna
• Biological source: Haemophilus influenzae; More
• Total number of polymer chains: 6
• Total formula weight: 69887.54

Authors

Horton, J.R. (deposition date: 2006-01-04, release date: 2006-02-21, Last modification date: 2023-08-30)

Primary citation

Horton, J.R.,Zhang, X.,Maunus, R.,Yang, Z.,Wilson, G.G.,Roberts, R.J.,Cheng, X.
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
Nucleic Acids Res., 34:939-948, 2006

PubMed Abstract: HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

PubMed: 16473850
DOI: 10.1093/nar/gkj484

Experimental method

X-RAY DIFFRACTION (2.39 Å)