Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease

Shao, Chen; Wang, Chengliang; Zang, Jianye

doi:10.1107/s139900471401606x

Cited by 14 publications

(19 citation statements)

References 50 publications

(68 reference statements)

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“…The cyanide groups in (I) adopt only a bidentate bridged geometry. The bridged C1-N1 distance of 1.142 (6) Å is typical for a cyanide C N bond length (Jia & Hou, 2012;Meng et al, 2012;Shao & Yu, 2014).…”

Section: Resultsmentioning

confidence: 99%

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

et al. 2016

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Square-planar complexes are commonly formed by transition metal ions having a d(8) electron configuration. Planar cyanometallate anions have been used extensively as design elements in supramolecular coordination systems. In particular, square-planar tetracyanometallate(II) ions, i.e. [M(CN)4](2-) (M(II) = Ni, Pd or Pt), are used as good building blocks for bimetallic Hofmann-type assemblies and their analogues. Square-planar tetracyanonickellate(II) complexes have been extensively developed with N-donor groups as additional co-ligands, but studies of these systems using O-donor ligands are scarce. A new cyanide-bridged Cu(II)-Ni(II) heterometallic compound, poly[[diaquatetra-μ2-cyanido-κ(8)C:N-nickel(II)copper(II)] monohydrate], {[Cu(II)Ni(II)(CN)4(H2O)2]·H2O}n, has been synthesized and characterized by X-ray single-crystal diffraction analyses, vibrational spectroscopy (FT-IR), thermal analysis, electron paramagnetic resonance (EPR) and magnetic moment measurements. The structural analysis revealed that it has a two-dimensional grid-like structure built up of cationic [Cu(H2O)2](2+) and anionic [Ni(CN)4](2-) units connected through bridging cyanide ligands. The overall three-dimensional supramolecular network is expanded by a combination of interlayer O-H...N and intralayer O-H...O hydrogen-bond interactions. The first decomposition reactions take place at 335 K under a static air atmosphere, which illustrates the existence of guest water molecules in the interlayer spaces. The electron paramagnetic resonance (EPR) spectrum confirms that the Cu(II) cation has an axial coordination symmetry and that the unpaired electrons occupy the d(x(2)-y(2)) orbital. In addition, magnetic investigations showed that antiferromagnetic interactions exist in the Cu(II) atoms through the diamagnetic [Ni(CN)4](2-) ion.

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Section: Resultsmentioning

confidence: 99%

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

et al. 2016

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“…These include MspJI, which recognizes 5mC and 5hmC (20), the PvuRts1I family, whose members show unique individual specificities for 5hmC and/or 5-glucosylhydroxymethylcytosine (5ghmC) (21), and GmrSD, which recognizes 5ghmC (22). Structural studies of McrB, MspJI, PvuRtsI, and AbaSI suggest type IV systems employ a generalized base-flipping mechanism for recognition of the modified DNA (23)(24)(25)(26)(27).…”

Section: This Work Was Supported By Cornell University and National Imentioning

confidence: 99%

The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding

Hosford

Chappie

2018

Journal of Biological Chemistry

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Restriction modification systems consist of an endonuclease that cleaves foreign DNA site-specifically and an associated methyltransferase that protects the corresponding target site in the host genome. Modification-dependent restriction systems, in contrast, specifically recognize and cleave methylated and/or glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC, respectively, which in function together as a modification-dependent restriction complex specific for 5mC-containing DNA. LlaJI.R1 binds DNA site-specifically, suggesting that the LlaJI system uses a different mode of substrate recognition. Here we present the structure of the N-terminal DNA-binding domain of LlaJI.R1 at 1.97-Å resolution, which adopts a B3 domain fold. Structural comparison to B3 domains in plant transcription factors and other restriction enzymes identifies key recognition motifs responsible for site-specific DNA binding. Moreover, biochemistry and structural modeling provide a rationale for how LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by other LlaJI homologs and identify residues critical for this recognition activity. These findings underscore the inherent structural plasticity of B3 domains, allowing recognition of a variety of substrates using the same structural core.

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“…Mutational analysis and close structural resemblance of DNA binding domains of AspBHI, PvuRts1I and AbaSI to the SRA domains of MspJI and eukaryotic proteins ( Fig. 1C-D ) suggest that these enzymes also flip-out the modified cytosine [18] , [20] – [23] .…”

Section: Introductionmentioning

confidence: 96%

“…Due to strict specificity for unmodified DNA and fixed cleavage positions, both MspJI- and PvuRts1I-like enzymes are used as molecular tools for single-base resolution mapping of 5mC and 5hmC modifications in eukaryotic genomes [16] , [17] . The recently solved structures of MspJI, AspBHI (MspJI family), PvuRts1I and AbaSI (PvuRts1I family) enzymes [18] – [23] revealed that these enzymes are comprised of a PD-(D/E)XK nuclease domain fused to a SRA-like DNA binding domain (DBD). The co-crystal structure of the MspJI-DNA complex demonstrated that MspJI flips-out 5-methylcytosine into a protein pocket where a set of base-specific contacts are made ( Fig.…”

Section: Introductionmentioning

confidence: 99%

Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families

Zagorskaitė

Sasnauskas

2014

PLoS ONE

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The epigenetic DNA modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in eukaryotes are recognized either in the context of double-stranded DNA (e.g., by the methyl-CpG binding domain of MeCP2), or in the flipped-out state (e.g., by the SRA domain of UHRF1). The SRA-like domains and the base-flipping mechanism for 5(h)mC recognition are also shared by the recently discovered prokaryotic modification-dependent endonucleases of the MspJI and PvuRts1I families. Since the mechanism of modified cytosine recognition by many potential eukaryotic and prokaryotic 5(h)mC “readers” is still unknown, a fast solution based method for the detection of extrahelical 5(h)mC would be very useful. In the present study we tested base-flipping by MspJI- and PvuRts1I-like restriction enzymes using several solution-based methods, including fluorescence measurements of the cytosine analog pyrrolocytosine and chemical modification of extrahelical pyrimidines with chloroacetaldehyde and KMnO4. We find that only KMnO4 proved an efficient probe for the positive display of flipped out pyrimidines, albeit the method required either non-physiological pH (4.3) or a substitution of the target cytosine with thymine. Our results imply that DNA recognition mechanism of 5(h)mC binding proteins should be tested using a combination of all available methods, as the lack of a positive signal in some assays does not exclude the base flipping mechanism.

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Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease

Abstract: The crystal structure of PvuRts1I was determined and a 5-hydroxymethylcytosine-binding pocket was identified in the SRA-like domain. Enzyme variants were engineered to assist in hydroxymethylome mapping based on the crystal structure of PvuRts1I.

Cited by 14 publications

References 50 publications

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding

Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families

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Structural basis for the substrate selectivity of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease

Abstract: The crystal structure of PvuRts1I was determined and a 5-hydroxymethylcytosine-binding pocket was identified in the SRA-like domain. Enzyme variants were engineered to assist in hydroxymethylome mapping based on the crystal structure of PvuRts1I.

Cited by 14 publications

References 50 publications

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)4]2−: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)4]2−: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding

Chemical Display of Pyrimidine Bases Flipped Out by Modification-Dependent Restriction Endonucleases of MspJI and PvuRts1I Families

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A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties

A cyanide-bridged heterometallic coordination polymer constructed from square-planar [Ni(CN)₄]²⁻: synthesis, crystal structure, thermal decomposition, electron paramagnetic resonance (EPR) spectrum and magnetic properties