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Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination.

Kang HA, Shin HC, Kalantzi AS, Toseland CP, Kim HM, Gruber S, Peraro MD, Oh BH - Nucleic Acids Res. (2015)

Bottom Line: One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra α-helices to form a helical bundle-like structure.Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament.Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.

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Juxtaposed WHDs and a model for dsDNA binding. (A) The interface between the WHDs is mostly hydrophobic. The residues at the interface are shown in sticks, with the hydrophobic residues labeled in red. The view is to look down from LZ1. (B) Superposition of the WHD pairs in Heterodimers I and II. The Cα traces were superposed only for Hop2. (C) Superposition of the WHD of TtgV bound to its recognition sequence (PDB entry: 2xro) onto each WHD of Hop2 and Mnd1. The arrow highlights the discontinuity of the DNA duplex. (D) A model for dsDNA binding to the WHD pair. The two dsDNA segments in C were connected to form a single dsDNA. The geometry was refined (see Methods section) and the resulting model is shown with the inset highlighting the observed dissociation of base pairs during ∼94 ns of MD simulation. Only the WHDs and LZ1 are included in the simulation. The view is to look down from LZ1. (E) MD-averaged base-pairing distances during ∼94 ns of MD simulation. Large deviations from canonical base-pairing geometries take place in the middle segment of dsDNA. (F) RMSDs between the crystal structure reference and each individual WHD and their heterodimer during the MD simulation time. RMSDs were calculated for all atoms. (G) RMSFs per residue during the simulation time. Much smaller fluctuation of the WHDs in comparison with LZ1 is noted. RMSFs were calculated for the Cα atoms only.
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Figure 5: Juxtaposed WHDs and a model for dsDNA binding. (A) The interface between the WHDs is mostly hydrophobic. The residues at the interface are shown in sticks, with the hydrophobic residues labeled in red. The view is to look down from LZ1. (B) Superposition of the WHD pairs in Heterodimers I and II. The Cα traces were superposed only for Hop2. (C) Superposition of the WHD of TtgV bound to its recognition sequence (PDB entry: 2xro) onto each WHD of Hop2 and Mnd1. The arrow highlights the discontinuity of the DNA duplex. (D) A model for dsDNA binding to the WHD pair. The two dsDNA segments in C were connected to form a single dsDNA. The geometry was refined (see Methods section) and the resulting model is shown with the inset highlighting the observed dissociation of base pairs during ∼94 ns of MD simulation. Only the WHDs and LZ1 are included in the simulation. The view is to look down from LZ1. (E) MD-averaged base-pairing distances during ∼94 ns of MD simulation. Large deviations from canonical base-pairing geometries take place in the middle segment of dsDNA. (F) RMSDs between the crystal structure reference and each individual WHD and their heterodimer during the MD simulation time. RMSDs were calculated for all atoms. (G) RMSFs per residue during the simulation time. Much smaller fluctuation of the WHDs in comparison with LZ1 is noted. RMSFs were calculated for the Cα atoms only.

Mentions: The two WHDs are closely juxtaposed and interact with each other (Figure 5A). The WHD–WHD interface, burying a surface area of 250.6 Å2, comprises of many hydrophobic residues (Pro22, Ile55, Leu65, Leu67 of Hop2; Ile25, Ile63, Tyr68, Trp70, Phe72 of Mnd1) and two charged residues (Lys21 of Hop2; Asp61 of Mnd1) forming a salt bridge (Figure 5A). These observations indicate that the WHDs adopt a fixed, rather than random, relative orientation. Consistent with this notion, the WHDs in Heterodimers I and II exhibit virtually the same orientations (Figure 5B). Remarkably, all of the interface lining residues are highly conserved except Ile55 of Hop2 (Figure 3A and B; orange boxes), indicating that the juxtaposition of the WHDs in the observed orientations is likely to be an evolutionary conserved feature important for the molecular function of Hop2–Mnd1. A further confirmation of the stability of the WHD–WHD interface comes from molecular dynamics (MD) simulations, as described in the next section.


Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination.

Kang HA, Shin HC, Kalantzi AS, Toseland CP, Kim HM, Gruber S, Peraro MD, Oh BH - Nucleic Acids Res. (2015)

Juxtaposed WHDs and a model for dsDNA binding. (A) The interface between the WHDs is mostly hydrophobic. The residues at the interface are shown in sticks, with the hydrophobic residues labeled in red. The view is to look down from LZ1. (B) Superposition of the WHD pairs in Heterodimers I and II. The Cα traces were superposed only for Hop2. (C) Superposition of the WHD of TtgV bound to its recognition sequence (PDB entry: 2xro) onto each WHD of Hop2 and Mnd1. The arrow highlights the discontinuity of the DNA duplex. (D) A model for dsDNA binding to the WHD pair. The two dsDNA segments in C were connected to form a single dsDNA. The geometry was refined (see Methods section) and the resulting model is shown with the inset highlighting the observed dissociation of base pairs during ∼94 ns of MD simulation. Only the WHDs and LZ1 are included in the simulation. The view is to look down from LZ1. (E) MD-averaged base-pairing distances during ∼94 ns of MD simulation. Large deviations from canonical base-pairing geometries take place in the middle segment of dsDNA. (F) RMSDs between the crystal structure reference and each individual WHD and their heterodimer during the MD simulation time. RMSDs were calculated for all atoms. (G) RMSFs per residue during the simulation time. Much smaller fluctuation of the WHDs in comparison with LZ1 is noted. RMSFs were calculated for the Cα atoms only.
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Related In: Results  -  Collection

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Show All Figures
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Figure 5: Juxtaposed WHDs and a model for dsDNA binding. (A) The interface between the WHDs is mostly hydrophobic. The residues at the interface are shown in sticks, with the hydrophobic residues labeled in red. The view is to look down from LZ1. (B) Superposition of the WHD pairs in Heterodimers I and II. The Cα traces were superposed only for Hop2. (C) Superposition of the WHD of TtgV bound to its recognition sequence (PDB entry: 2xro) onto each WHD of Hop2 and Mnd1. The arrow highlights the discontinuity of the DNA duplex. (D) A model for dsDNA binding to the WHD pair. The two dsDNA segments in C were connected to form a single dsDNA. The geometry was refined (see Methods section) and the resulting model is shown with the inset highlighting the observed dissociation of base pairs during ∼94 ns of MD simulation. Only the WHDs and LZ1 are included in the simulation. The view is to look down from LZ1. (E) MD-averaged base-pairing distances during ∼94 ns of MD simulation. Large deviations from canonical base-pairing geometries take place in the middle segment of dsDNA. (F) RMSDs between the crystal structure reference and each individual WHD and their heterodimer during the MD simulation time. RMSDs were calculated for all atoms. (G) RMSFs per residue during the simulation time. Much smaller fluctuation of the WHDs in comparison with LZ1 is noted. RMSFs were calculated for the Cα atoms only.
Mentions: The two WHDs are closely juxtaposed and interact with each other (Figure 5A). The WHD–WHD interface, burying a surface area of 250.6 Å2, comprises of many hydrophobic residues (Pro22, Ile55, Leu65, Leu67 of Hop2; Ile25, Ile63, Tyr68, Trp70, Phe72 of Mnd1) and two charged residues (Lys21 of Hop2; Asp61 of Mnd1) forming a salt bridge (Figure 5A). These observations indicate that the WHDs adopt a fixed, rather than random, relative orientation. Consistent with this notion, the WHDs in Heterodimers I and II exhibit virtually the same orientations (Figure 5B). Remarkably, all of the interface lining residues are highly conserved except Ile55 of Hop2 (Figure 3A and B; orange boxes), indicating that the juxtaposition of the WHDs in the observed orientations is likely to be an evolutionary conserved feature important for the molecular function of Hop2–Mnd1. A further confirmation of the stability of the WHD–WHD interface comes from molecular dynamics (MD) simulations, as described in the next section.

Bottom Line: One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra α-helices to form a helical bundle-like structure.Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament.Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, KAIST Institute for the Biocentury, Cancer Metastasis Control Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.

Show MeSH
Related in: MedlinePlus