1YNM

Crystal structure of restriction endonuclease HinP1I

Summary for 1YNM

• Entry DOI: 10.2210/pdb1ynm/pdb
• Descriptor: R.HinP1I restriction endonuclease (2 entities in total)
• Functional Keywords: restriction endonuclease, dimerizaton, hydrolase
• Biological source: Haemophilus influenzae
• Total number of polymer chains: 1
• Total formula weight: 28791.67

Authors

Yang, Z.,Horton, J.R.,Maunus, R.,Wilson, G.G.,Roberts, R.J.,Cheng, X. (deposition date: 2005-01-24, release date: 2005-05-03, Last modification date: 2024-02-14)

Primary citation

Yang, Z.,Horton, J.R.,Maunus, R.,Wilson, G.G.,Roberts, R.J.,Cheng, X.
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI
Nucleic Acids Res., 33:1892-1901, 2005

PubMed Abstract: HinP1I, a type II restriction endonuclease, recognizes and cleaves a palindromic tetranucleotide sequence (G/CGC) in double-stranded DNA, producing 2 nt 5' overhanging ends. Here, we report the structure of HinP1I crystallized as one protein monomer in the crystallographic asymmetric unit. HinP1I displays an elongated shape, with a conserved catalytic core domain containing an active-site motif of SDX18QXK and a putative DNA-binding domain. Without significant sequence homology, HinP1I displays striking structural similarity to MspI, an endonuclease that cleaves a similar palindromic DNA sequence (C/CGG) and binds to that sequence crystallographically as a monomer. Almost all the structural elements of MspI can be matched in HinP1I, including both the DNA recognition and catalytic elements. Examining the protein-protein interactions in the crystal lattice, HinP1I could be dimerized through two helices located on the opposite side of the protein to the active site, generating a molecule with two active sites and two DNA-binding surfaces opposite one another on the outer surfaces of the dimer. A possible functional link between this unusual dimerization mode and the tetrameric restriction enzymes is discussed.

PubMed: 15805123
DOI: 10.1093/nar/gki337

Experimental method

X-RAY DIFFRACTION (2.65 Å)