6GHS

Modification dependent TagI restriction endonuclease

Summary for 6GHS

• Entry DOI: 10.2210/pdb6ghs/pdb
• Descriptor: TagI restriction endonuclease, ZINC ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: restriction endonuclease, type ii, type iv, cytosine modification, 5-methylcytosine, 5mc, 5-hydroxymethylcytosine, 5hmc, sra, hnh, bba-me nuclease, scoa3iv, sco5333, tbir51i, tbis1, hydrolase
• Biological source: Thermocrispum agreste
• Total number of polymer chains: 1
• Total formula weight: 34085.57

Authors

Kisiala, M.,Copelas, A.,Czapinska, H.,Xu, S.,Bochtler, M. (deposition date: 2018-05-08, release date: 2018-08-29, Last modification date: 2024-01-17)

Primary citation

Kisiala, M.,Copelas, A.,Czapinska, H.,Xu, S.Y.,Bochtler, M.
Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.
Nucleic Acids Res., 46:10489-10503, 2018

PubMed Abstract: TagI belongs to the recently characterized SRA-HNH family of modification-dependent restriction endonucleases (REases) that also includes ScoA3IV (Sco5333) and TbiR51I (Tbis1). Here, we present a crystal structure of dimeric TagI, which exhibits a DNA binding site formed jointly by the nuclease domains, and separate binding sites for modified DNA bases in the two protomers. The nuclease domains have characteristic features of HNH/ββα-Me REases, and catalyze nicks or double strand breaks, with preference for /RY and RYN/RY sites, respectively. The SRA domains have the canonical fold. Their pockets for the flipped bases are spacious enough to accommodate 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC), but not glucosyl-5-hydroxymethylcytosine (g5hmC). Such preference is in agreement with the biochemical determination of the TagI modification dependence and the results of phage restriction assays. The ability of TagI to digest plasmids methylated by Dcm (C5mCWGG), M.Fnu4HI (G5mCNGC) or M.HpyCH4IV (A5mCGT) suggests that the SRA domains of the enzyme are tolerant to different sequence contexts of the modified base.

PubMed: 30202937
DOI: 10.1093/nar/gky781

Experimental method

X-RAY DIFFRACTION (2.92 Å)