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Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.

Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X - Nucleic Acids Res. (2005)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA.

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.

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Structure of HinP1I (A) Ribbon representation. Helices are labeled as letters A–H and strands labeled as numbers 1–11 from N- to C-termini. Putative catalytic residues are shown in magenta color. The C-terminal β-hairpin, colored in red, contains the invariant residues (presumably involved in DNA base specific interactions) between HinP1I and MspI. (B) Molecular surface representation, shown in the same orientation of (A). The surface is colored blue for positive, red for negative and white for neutral. The basic (blue) concave surface, shown on the right side of the molecule, represents a DNA-binding surface. Several conserved charged residues (labeled) are scattered throughout the surface. R168, shown on the left side of the molecule, represents a potential dimer interface (see Figure 5B). (C) Superimposition of HinP1I (green) and MspI (cyan). (D) A model of HinP1I monomer docked with DNA.
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fig2: Structure of HinP1I (A) Ribbon representation. Helices are labeled as letters A–H and strands labeled as numbers 1–11 from N- to C-termini. Putative catalytic residues are shown in magenta color. The C-terminal β-hairpin, colored in red, contains the invariant residues (presumably involved in DNA base specific interactions) between HinP1I and MspI. (B) Molecular surface representation, shown in the same orientation of (A). The surface is colored blue for positive, red for negative and white for neutral. The basic (blue) concave surface, shown on the right side of the molecule, represents a DNA-binding surface. Several conserved charged residues (labeled) are scattered throughout the surface. R168, shown on the left side of the molecule, represents a potential dimer interface (see Figure 5B). (C) Superimposition of HinP1I (green) and MspI (cyan). (D) A model of HinP1I monomer docked with DNA.

Mentions: HinP1I comprises 247 amino acids, the first six N-terminal residues of which are invisible in the electron density map. In overall topology, HinP1I belongs to the α/β protein class, with elongated dimensions of 68 × 33 × 32 Å (Figure 2A), and contains two sets of β-sheets surrounded by eight α helices. The upper β-sheet is a mixed six-stranded (β1-7-6-4-3-2) sheet sandwiched by four α helices (αA and αB on one side, and αH and αG on the other). The lower sheet contains five anti-parallel strands (β5-11-10-9-8), with the left side of the sheet packing against five α helices (αC, αD, αE, αF and αG) and the right side forming a concave basic surface, which is the putative DNA-binding site (Figure 2B).


Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.

Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X - Nucleic Acids Res. (2005)

Structure of HinP1I (A) Ribbon representation. Helices are labeled as letters A–H and strands labeled as numbers 1–11 from N- to C-termini. Putative catalytic residues are shown in magenta color. The C-terminal β-hairpin, colored in red, contains the invariant residues (presumably involved in DNA base specific interactions) between HinP1I and MspI. (B) Molecular surface representation, shown in the same orientation of (A). The surface is colored blue for positive, red for negative and white for neutral. The basic (blue) concave surface, shown on the right side of the molecule, represents a DNA-binding surface. Several conserved charged residues (labeled) are scattered throughout the surface. R168, shown on the left side of the molecule, represents a potential dimer interface (see Figure 5B). (C) Superimposition of HinP1I (green) and MspI (cyan). (D) A model of HinP1I monomer docked with DNA.
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fig2: Structure of HinP1I (A) Ribbon representation. Helices are labeled as letters A–H and strands labeled as numbers 1–11 from N- to C-termini. Putative catalytic residues are shown in magenta color. The C-terminal β-hairpin, colored in red, contains the invariant residues (presumably involved in DNA base specific interactions) between HinP1I and MspI. (B) Molecular surface representation, shown in the same orientation of (A). The surface is colored blue for positive, red for negative and white for neutral. The basic (blue) concave surface, shown on the right side of the molecule, represents a DNA-binding surface. Several conserved charged residues (labeled) are scattered throughout the surface. R168, shown on the left side of the molecule, represents a potential dimer interface (see Figure 5B). (C) Superimposition of HinP1I (green) and MspI (cyan). (D) A model of HinP1I monomer docked with DNA.
Mentions: HinP1I comprises 247 amino acids, the first six N-terminal residues of which are invisible in the electron density map. In overall topology, HinP1I belongs to the α/β protein class, with elongated dimensions of 68 × 33 × 32 Å (Figure 2A), and contains two sets of β-sheets surrounded by eight α helices. The upper β-sheet is a mixed six-stranded (β1-7-6-4-3-2) sheet sandwiched by four α helices (αA and αB on one side, and αH and αG on the other). The lower sheet contains five anti-parallel strands (β5-11-10-9-8), with the left side of the sheet packing against five α helices (αC, αD, αE, αF and αG) and the right side forming a concave basic surface, which is the putative DNA-binding site (Figure 2B).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA.

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.

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