Limits...
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.

Show MeSH
Structural similarity between HinP1I and MspI (A) Schematic diagram of MspI–DNA interactions, reproduced and modified from Xu et al. (5). Solid lines indicate direct hydrogen bonds, dotted lines indicate water-mediated hydrogen bonds and ‘mc’ indicates interaction involving main chain atom. (B) Residues potentially important for DNA base specific recognition: superimposition of residues of HinP1I (green) and MspI (cyan). (C) Residues potentially important for catalysis: superimposition of active site residues of HinP1I (green), MspI (cyan) and EcoRV (grey). Four residues belong to a common motif of E……PDX15DXK (EcoRV), E……SDX18QXK (HinP1I) and E……TDX17NXK (MspI).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC1074309&req=5

fig4: Structural similarity between HinP1I and MspI (A) Schematic diagram of MspI–DNA interactions, reproduced and modified from Xu et al. (5). Solid lines indicate direct hydrogen bonds, dotted lines indicate water-mediated hydrogen bonds and ‘mc’ indicates interaction involving main chain atom. (B) Residues potentially important for DNA base specific recognition: superimposition of residues of HinP1I (green) and MspI (cyan). (C) Residues potentially important for catalysis: superimposition of active site residues of HinP1I (green), MspI (cyan) and EcoRV (grey). Four residues belong to a common motif of E……PDX15DXK (EcoRV), E……SDX18QXK (HinP1I) and E……TDX17NXK (MspI).

Mentions: Almost all the structural elements of HinP1I can be matched in MspI (Figure 2C), including both the DNA recognition elements and the catalytic elements. This near-perfect match allowed us to create a model of HinP1I bound to DNA (Figure 2D). Using the coordinates for the complex of MspI–DNA (see Figure 1D), we superimposed the protein components and then positioned the DNA over the basic concave surface. The resulting model showed that HinP1I could contact the DNA without physical distortion of either the protein or the DNA component. Besides an extra N-terminal helix in MspI and an extra C-terminal helix in HinP1I (Figure 3), the most obvious differences between the two structures are helix αA, which is three helical turns longer in MspI and inserts into the minor groove of DNA to make water-mediated hydrogen bonds with the recognition sequence, and the loop between helices αD and αE, which is 13 residue longer in HinP1I and could adopt a closed conformation upon association with DNA (Figure 2C). The shorter corresponding loop in MspI (residues D157–K161) is involved in phosphate contacts outside of the recognition sequence (Figure 4A).


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)

Structural similarity between HinP1I and MspI (A) Schematic diagram of MspI–DNA interactions, reproduced and modified from Xu et al. (5). Solid lines indicate direct hydrogen bonds, dotted lines indicate water-mediated hydrogen bonds and ‘mc’ indicates interaction involving main chain atom. (B) Residues potentially important for DNA base specific recognition: superimposition of residues of HinP1I (green) and MspI (cyan). (C) Residues potentially important for catalysis: superimposition of active site residues of HinP1I (green), MspI (cyan) and EcoRV (grey). Four residues belong to a common motif of E……PDX15DXK (EcoRV), E……SDX18QXK (HinP1I) and E……TDX17NXK (MspI).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1074309&req=5

fig4: Structural similarity between HinP1I and MspI (A) Schematic diagram of MspI–DNA interactions, reproduced and modified from Xu et al. (5). Solid lines indicate direct hydrogen bonds, dotted lines indicate water-mediated hydrogen bonds and ‘mc’ indicates interaction involving main chain atom. (B) Residues potentially important for DNA base specific recognition: superimposition of residues of HinP1I (green) and MspI (cyan). (C) Residues potentially important for catalysis: superimposition of active site residues of HinP1I (green), MspI (cyan) and EcoRV (grey). Four residues belong to a common motif of E……PDX15DXK (EcoRV), E……SDX18QXK (HinP1I) and E……TDX17NXK (MspI).
Mentions: Almost all the structural elements of HinP1I can be matched in MspI (Figure 2C), including both the DNA recognition elements and the catalytic elements. This near-perfect match allowed us to create a model of HinP1I bound to DNA (Figure 2D). Using the coordinates for the complex of MspI–DNA (see Figure 1D), we superimposed the protein components and then positioned the DNA over the basic concave surface. The resulting model showed that HinP1I could contact the DNA without physical distortion of either the protein or the DNA component. Besides an extra N-terminal helix in MspI and an extra C-terminal helix in HinP1I (Figure 3), the most obvious differences between the two structures are helix αA, which is three helical turns longer in MspI and inserts into the minor groove of DNA to make water-mediated hydrogen bonds with the recognition sequence, and the loop between helices αD and αE, which is 13 residue longer in HinP1I and could adopt a closed conformation upon association with DNA (Figure 2C). The shorter corresponding loop in MspI (residues D157–K161) is involved in phosphate contacts outside of the recognition sequence (Figure 4A).

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.

Show MeSH