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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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A hypothetical model of a HinP1I dimer bound with a single copy of DNA. The two monomers of Hinp1I are shown in green and magenta. (A) The presentation of green monomer of Hinp1I is similar to that shown in Figure 2D. (B) A view looking into the DNA major groove.
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fig7: A hypothetical model of a HinP1I dimer bound with a single copy of DNA. The two monomers of Hinp1I are shown in green and magenta. (A) The presentation of green monomer of Hinp1I is similar to that shown in Figure 2D. (B) A view looking into the DNA major groove.

Mentions: We do not know whether the solution properties of HinP1I are dependent on the presence of substrate DNA, although, most of the structurally characterized type II endonuclease–DNA complexes comprise a protein dimer of identical subunits and a single copy of a double-stranded oligonucleotide, with one active site for each DNA strand. Certain type IIS enzymes, such as FokI, dimerize transiently during catalysis (6,15,38) and it seems reasonable to assume that HinP1I would, too. We attempted to create a model of the HinP1I dimer bound to a single copy of DNA. To prepare the model, we rotated the HinP1I monomer (green) along the 2-fold symmetry of the palindromic DNA and generated the second monomer (magenta) with its active site for the other strand (Figure 7). The most serious steric clash occurs between helices αC and αD of one monomer and their 2-fold symmetry-related counterparts of the other monomer. We imagine that upon associating with DNA, helices αC and αD could adopt a different non-clashing conformation that would allow the formation of an anti-parallel four-helix bundle in the dimer interface. Interestingly, helix αD contains two invariant residues between HinP1I (D109 and R117) and MspI (D144 and R152) (see Figures 3), whose positions are exposed on the monomer surface (see Figure 2B), and which might therefore participate in face-to-face dimerization much as such residues do in the back-to-back dimerization discussed earlier.


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)

A hypothetical model of a HinP1I dimer bound with a single copy of DNA. The two monomers of Hinp1I are shown in green and magenta. (A) The presentation of green monomer of Hinp1I is similar to that shown in Figure 2D. (B) A view looking into the DNA major groove.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1074309&req=5

fig7: A hypothetical model of a HinP1I dimer bound with a single copy of DNA. The two monomers of Hinp1I are shown in green and magenta. (A) The presentation of green monomer of Hinp1I is similar to that shown in Figure 2D. (B) A view looking into the DNA major groove.
Mentions: We do not know whether the solution properties of HinP1I are dependent on the presence of substrate DNA, although, most of the structurally characterized type II endonuclease–DNA complexes comprise a protein dimer of identical subunits and a single copy of a double-stranded oligonucleotide, with one active site for each DNA strand. Certain type IIS enzymes, such as FokI, dimerize transiently during catalysis (6,15,38) and it seems reasonable to assume that HinP1I would, too. We attempted to create a model of the HinP1I dimer bound to a single copy of DNA. To prepare the model, we rotated the HinP1I monomer (green) along the 2-fold symmetry of the palindromic DNA and generated the second monomer (magenta) with its active site for the other strand (Figure 7). The most serious steric clash occurs between helices αC and αD of one monomer and their 2-fold symmetry-related counterparts of the other monomer. We imagine that upon associating with DNA, helices αC and αD could adopt a different non-clashing conformation that would allow the formation of an anti-parallel four-helix bundle in the dimer interface. Interestingly, helix αD contains two invariant residues between HinP1I (D109 and R117) and MspI (D144 and R152) (see Figures 3), whose positions are exposed on the monomer surface (see Figure 2B), and which might therefore participate in face-to-face dimerization much as such residues do in the back-to-back dimerization discussed earlier.

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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