ArticleJournal of molecular biology2008
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Eliminating the type I restriction endonuclease fromMicrobiology (Reading, England) · 2025Article
- Bacterial restriction-modification systems: mechanisms of defense against phage infection.Biophysics reports · 2025Article
- The group AInfection and immunity · 2025Article
- Genomic epidemiological analysis reveals new insights into the resurgence ofFrontiers in cellular and infection microbiology · 2025Article
- Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium.Nature microbiology · 2025Article
- Article
- Developing a genetic engineering method for Acetobacterium wieringae to expand one-carbon valorization pathways.Biotechnology for biofuels and bioproducts · 2023Article
- Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from ProbioticViruses · 2019Article
- Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.The Journal of biological chemistry · 2018Article
- Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures.European biophysics journal : EBJ · 2017Article
- The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation.PeerJ · 2017Article
- pHluorin-assisted expression, purification, crystallization and X-ray diffraction data analysis of the C-terminal domain of the HsdR subunit of the Escherichia coli type I restriction-modification system EcoR124I.Acta crystallographica. Section F, Structural biology communications · 2016Article
- As Clear as Mud? Determining the Diversity and Prevalence of Prophages in the Draft Genomes of Estuarine Isolates of Clostridium difficile.Genome biology and evolution · 2015Article
- Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme.PloS one · 2015Article
- DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis.Nucleic acids research · 2014Article
- Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.Journal of molecular modeling · 2014Article
- Structural and functional analysis of the symmetrical Type I restriction endonuclease R.EcoR124IPloS one · 2012Article
- Structure and operation of the DNA-translocating type I DNA restriction enzymes.Genes & development · 2012Article
- An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI.Nucleic acids research · 2009Article
- The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.Nucleic acids research · 2009Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
Type I restriction-modification (RM) systems are large, multifunctional enzymes composed of three different subunits. HsdS and HsdM form a complex in which HsdS recognizes the target DNA sequence, and HsdM carries out methylation of adenosine residues. The HsdR subunit, when associated with the HsdS-HsdM complex, translocates DNA in an ATP-dependent process and cleaves unmethylated DNA at a distance of several thousand base-pairs from the recognition site. The molecular mechanism by which these enzymes translocate the DNA is not fully understood, in part because of the absence of crystal structures. To date, crystal structures have been determined for the individual HsdS and HsdM subunits and models have been built for the HsdM-HsdS complex with the DNA. However, no structure is available for the HsdR subunit. In this work, the gene coding for the HsdR subunit of EcoR124I was re-sequenced, which showed that there was an error in the published sequence. This changed the position of the stop codon and altered the last 17 amino acid residues of the protein sequence. An improved purification procedure was developed to enable HsdR to be purified efficiently for biophysical and structural analysis. Analytical ultracentrifugation shows that HsdR is monomeric in solution, and the frictional ratio of 1.21 indicates that the subunit is globular and fairly compact. Small angle neutron-scattering of the HsdR subunit indicates a radius of gyration of 3.4 nm and a maximum dimension of 10 nm. We constructed a model of the HsdR using protein fold-recognition and homology modelling to model individual domains, and small-angle neutron scattering data as restraints to combine them into a single molecule. The model reveals an ellipsoidal shape of the enzymatic core comprising the N-terminal and central domains, and suggests conformational heterogeneity of the C-terminal region implicated in binding of HsdR to the HsdS-HsdM complex.
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