6P0F

N-terminal domain of Thermococcus Gammatolerans McrB

Summary for 6P0F

• Entry DOI: 10.2210/pdb6p0f/pdb
• Descriptor: GTPase subunit of restriction endonuclease, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, SULFATE ION, ... (5 entities in total)
• Functional Keywords: yth domain, restriction endonuclease, dna binding protein
• Biological source: Thermococcus gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)
• Total number of polymer chains: 1
• Total formula weight: 22046.56

Authors

Hosford, C.J.,Chappie, J.S. (deposition date: 2019-05-17, release date: 2019-12-18, Last modification date: 2024-10-23)

Primary citation

Hosford, C.J.,Bui, A.Q.,Chappie, J.S.
The structure of theThermococcus gammatoleransMcrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs.
J.Biol.Chem., 295:743-756, 2020

PubMed Abstract: McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.

PubMed: 31822563
DOI: 10.1074/jbc.RA119.010188

Experimental method

X-RAY DIFFRACTION (1.683 Å)