(Q33885645)

29 July 2017

title

HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling (English)

1 reference

29 July 2017

5

Janusz M Bujnicki

1 reference

29 July 2017

author name string

Agnieszka Obarska-Kosinska

1

1 reference

29 July 2017

James E Taylor

2

1 reference

29 July 2017

Philip Callow

3

1 reference

29 July 2017

Jerzy Orlowski

4

1 reference

29 July 2017

G Geoff Kneale

6

1 reference

29 July 2017

language of work or name

English

0 references

publication date

17 November 2007

1 reference

Journal of Molecular Biology

29 July 2017

published in

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29 July 2017

volume

376

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29 July 2017

issue

2

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29 July 2017

page(s)

438-452

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Shape and subunit organisation of the DNA methyltransferase M.AhdI by small-angle neutron scattering

29 July 2017

cites work

1 reference

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A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering

5 July 2018

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REBASE--enzymes and genes for DNA restriction and modification

5 July 2018

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Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa

5 July 2018

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Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.

5 July 2018

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5 July 2018

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FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

5 July 2018

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5 July 2018

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5 July 2018

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REPPER--repeats and their periodicities in fibrous proteins

5 July 2018

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5 July 2018

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Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications

5 July 2018

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Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site

5 July 2018

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A homology model of restriction endonuclease SfiI in complex with DNA

5 July 2018

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Crystal structure of the human ATP-dependent splicing and export factor UAP56.

5 July 2018

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Protein homology detection by HMM-HMM comparison

5 July 2018

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Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA splicing and mRNA export

5 July 2018

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COLORADO3D, a web server for the visual analysis of protein structures.

5 July 2018

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S-Adenosyl-L-methionine-dependent restriction enzymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Modeling structurally variable regions in homologous proteins with rosetta.

5 July 2018

1 reference

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

5 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

A ?FRankenstein's monster? approach to comparative modeling: Merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Chemical cross-linking and mass spectrometry for protein structural modeling.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

GeneSilico protein structure prediction meta-server.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Can correct protein models be identified?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

CDD: a curated Entrez database of conserved domain alignments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Estimation of inter-residue distances in spin labeled proteins at physiological temperatures: experimental strategies and practical limitations.

5 July 2018

1 reference

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Pcons: a neural-network-based consensus predictor that improves fold recognition.

5 July 2018

1 reference

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Nucleoside triphosphate-dependent restriction enzymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Comparative protein structure modeling of genes and genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Size-Distribution Analysis of Macromolecules by Sedimentation Velocity Ultracentrifugation and Lamm Equation Modeling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Analysis of the subunit assembly of the typeIC restriction-modification enzyme EcoR124I

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Protein-protein and protein-DNA interactions in the type I restriction endonuclease R.EcoR124I.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Protein hydration in solution: experimental observation by x-ray and neutron scattering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Protein structure comparison by alignment of distance matrices

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

ATP Hydrolysis by Restriction Endonuclease from E. coli K

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

The EcoR124 and EcoR124/3 restriction and modification systems: cloning the genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Model for how type I restriction enzymes select cleavage sites in DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition

5 July 2018

1 reference

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Identification of correct regions in protein models using structural, alignment, and consensus information

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

The crystal structure of the UvsW helicase from bacteriophage T4.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2878639

On the structure and operation of type I DNA restriction enzymes

29 October 2018

1 reference

12 December 2020

Optimizing long intrinsic disorder predictors with protein evolutionary information

1 reference

12 December 2020

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces

1 reference

12 December 2020

Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium

1 reference

12 December 2020

Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity

1 reference

12 December 2020

10.1016/J.JMB.2007.11.024

Identifiers

DOI

1 reference

29 July 2017

1 reference

29 July 2017

1 reference