Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA (Q27684070)

1

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6 June 2020

author name string

Janine G Borgaro

2

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6 June 2020

Rose M Griggs

3

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6 June 2020

Aine Quimby

4

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6 June 2020

Shengxi Guan

5

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6 June 2020

Xing Zhang

6

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6 June 2020

Geoffrey G Wilson

7

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6 June 2020

Yu Zheng

8

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6 June 2020

Zhenyu Zhu

9

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6 June 2020

Xiaodong Cheng

10

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6 June 2020

language of work or name

English

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publication date

July 2014

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published in

Nucleic Acids Research

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6 June 2020

volume

42

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24895434%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

page(s)

7947-7959

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6 June 2020

issue

12

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24895434%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution-NonCommercial 3.0 Unported

6 June 2020

copyright license

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Crystal structure of the 5hmC specific endonuclease PvuRts1I

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Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI

20 March 2017

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Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

20 March 2017

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Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation

20 March 2017

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Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization

20 March 2017

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Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation

20 March 2017

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Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

20 March 2017

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Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease

20 March 2017

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Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

20 March 2017

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Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation

20 March 2017

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Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family

20 March 2017

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Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites

20 March 2017

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Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

20 March 2017

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Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

20 March 2017

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Characterization and crystal structure of the type IIG restriction endonuclease RM.BpuSI

20 March 2017

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A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo

20 March 2017

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Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI

20 March 2017

1 reference

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Unusual Target Site Disruption by the Rare-Cutting HNH Restriction Endonuclease PacI

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

PHENIX: a comprehensive Python-based system for macromolecular structure solution

20 March 2017

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Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1

20 March 2017

1 reference

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The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix

20 March 2017

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DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion

20 March 2017

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Crystal structure of NaeI--an evolutionary bridge between DNA endonuclease and topoisomerase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Crystallographic and functional studies of very short patch repair endonuclease

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The role of metals in catalysis by the restriction endonuclease BamHI

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structure of the multimodular endonuclease FokI bound to DNA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

HhaI methyltransferase flips its target base out of the DNA helix

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structure of PvuII endonuclease with cognate DNA

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Dali server: conservation mapping in 3D

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Optimal description of a protein structure in terms of multiple groups undergoing TLS motion

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Coot: model-building tools for molecular graphics

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Cofactor requirement of HpyAV restriction endonuclease

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Multiparametric scaling of diffraction intensities

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

A unique family of Mrr-like modification-dependent restriction endonucleases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

A molecular viewer for the analysis of TLS rigid-body motion in macromolecules

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Type II restriction endonucleases: structure and mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Structure of restriction endonuclease BamHI and its relationship to EcoRI.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Substrate dependence of the mechanism of EcoRI endonuclease

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5-hydroxymethylcytosine.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Nucleophile activation in PD...(D/E)xK metallonucleases: an experimental and computational pK(a) study

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Molecular cloning and expression of a novel hydroxymethylcytosine-specific restriction enzyme (PvuRts1I) modulated by glucosylation of DNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Mutation of asparagine 229 to aspartate in thymidylate synthase converts the enzyme to a deoxycytidylate methylase

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

Recognition of structural perturbations in DNA by human DNA(cytosine-5)methyltransferase.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081097

FokI requires two specific DNA sites for cleavage

27 November 2018

1 reference

12 December 2020

DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites

1 reference

12 December 2020

Mechanism of T4 phage restriction by plasmid Rts 1. Cleavage of T4 phage DNA by Rts 1-specific enzyme

1 reference

12 December 2020

Kinetic and catalytic mechanism of HhaI methyltransferase

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU497

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24895434%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24895434%20AND%20SRC:MED&resulttype=core&format=json

6 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24895434%20AND%20SRC:MED&resulttype=core&format=json