6H2J

Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain

Summary for 6H2J

• Entry DOI: 10.2210/pdb6h2j/pdb
• Descriptor: Type I restriction enzyme R Protein, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: ecor124, hsdr, c-terminal domain, restriction-modification enzyme, endonuclease, escherichia coli, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 243027.63

Authors

Grinkevich, P.,Mesters, J.R.,Ettrich, R.H. (deposition date: 2018-07-13, release date: 2018-08-08, Last modification date: 2024-10-23)

Primary citation

Grinkevich, P.,Sinha, D.,Iermak, I.,Guzanova, A.,Weiserova, M.,Ludwig, J.,Mesters, J.R.,Ettrich, R.H.
Crystal structure of a novel domain of the motor subunit of the Type I restriction enzyme EcoR124 involved in complex assembly and DNA binding.
J. Biol. Chem., 293:15043-15054, 2018

PubMed Abstract: Although EcoR124 is one of the better-studied Type I restriction-modification enzymes, it still presents many challenges to detailed analyses because of its structural and functional complexity and missing structural information. In all available structures of its motor subunit HsdR, responsible for DNA translocation and cleavage, a large part of the HsdR C terminus remains unresolved. The crystal structure of the C terminus of HsdR, obtained with a crystallization chaperone in the form of pHluorin fusion and refined to 2.45 Å, revealed that this part of the protein forms an independent domain with its own hydrophobic core and displays a unique α-helical fold. The full-length HsdR model, based on the WT structure and the C-terminal domain determined here, disclosed a proposed DNA-binding groove lined by positively charged residues. and assays with a C-terminal deletion mutant of HsdR supported the idea that this domain is involved in complex assembly and DNA binding. Conserved residues identified through sequence analysis of the C-terminal domain may play a key role in protein-protein and protein-DNA interactions. We conclude that the motor subunit of EcoR124 comprises five structural and functional domains, with the fifth, the C-terminal domain, revealing a unique fold characterized by four conserved motifs in the IC subfamily of Type I restriction-modification systems. In summary, the structural and biochemical results reported here support a model in which the C-terminal domain of the motor subunit HsdR of the endonuclease EcoR124 is involved in complex assembly and DNA binding.

PubMed: 30054276
DOI: 10.1074/jbc.RA118.003978

Experimental method

X-RAY DIFFRACTION (2.6 Å)