6C5D
N-terminal domain of Helicobacter pylori LlaJI.R1
Summary for 6C5D
| Entry DOI | 10.2210/pdb6c5d/pdb |
| Descriptor | LlaJI.R1 (2 entities in total) |
| Functional Keywords | b3 domain, restriction endonuclease, dna binding protein |
| Biological source | Helicobacter pylori (Campylobacter pylori J99) |
| Total number of polymer chains | 4 |
| Total formula weight | 68024.95 |
| Authors | Hosford, C.J.,Chappie, J.S. (deposition date: 2018-01-16, release date: 2018-06-27, Last modification date: 2024-10-23) |
| Primary citation | Hosford, C.J.,Chappie, J.S. The crystal structure of theHelicobacter pyloriLlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. J. Biol. Chem., 293:11758-11771, 2018 Cited by PubMed Abstract: Restriction modification systems consist of an endonuclease that cleaves foreign DNA site-specifically and an associated methyltransferase that protects the corresponding target site in the host genome. Modification-dependent restriction systems, in contrast, specifically recognize and cleave methylated and/or glucosylated DNA. The LlaJI restriction system contains two 5-methylcytosine (5mC) methyltransferases (LlaJI.M1 and LlaJI.M2) and two restriction proteins (LlaJI.R1 and LlaJI.R2). LlaJI.R1 and LlaJI.R2 are homologs of McrB and McrC, respectively, which in function together as a modification-dependent restriction complex specific for 5mC-containing DNA. LlaJI.R1 binds DNA site-specifically, suggesting that the LlaJI system uses a different mode of substrate recognition. Here we present the structure of the N-terminal DNA-binding domain of LlaJI.R1 at 1.97-Å resolution, which adopts a B3 domain fold. Structural comparison to B3 domains in plant transcription factors and other restriction enzymes identifies key recognition motifs responsible for site-specific DNA binding. Moreover, biochemistry and structural modeling provide a rationale for how LlaJI.R1 may bind a target site that differs from the 5-bp sequence recognized by other LlaJI homologs and identify residues critical for this recognition activity. These findings underscore the inherent structural plasticity of B3 domains, allowing recognition of a variety of substrates using the same structural core. PubMed: 29895618DOI: 10.1074/jbc.RA118.001888 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.97 Å) |
Structure validation
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