6N0S

N-terminal domain of Staphylothermus marinus McrB

Summary for 6N0S

• Entry DOI: 10.2210/pdb6n0s/pdb
• Descriptor: ATPase associated with various cellular activities, AAA_5, SULFATE ION (3 entities in total)
• Functional Keywords: eve domain, restriction endonuclease, dna binding protein
• Biological source: Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1)
• Total number of polymer chains: 1
• Total formula weight: 21773.75

Authors

Hosford, C.J.,Niu, Y.,Chappie, J.S. (deposition date: 2018-11-07, release date: 2019-11-13, Last modification date: 2024-10-16)

Primary citation

Hosford, C.J.,Adams, M.C.,Niu, Y.,Chappie, J.S.
The N-terminal domain of Staphylothermus marinus McrB shares structural homology with PUA-like RNA binding proteins.
J.Struct.Biol., 211:107572-107572, 2020

PubMed Abstract: McrBC is a conserved modification-dependent restriction system that in Escherichia coli specifically targets foreign DNA containing methylated cytosines. Crystallographic data show that the N-terminal domain of Escherichia coli McrB binds substrates via a base flipping mechanism. This region is poorly conserved among the plethora of McrB homologs, suggesting that other species may use alternative binding strategies and/or recognize different targets. Here we present the crystal structure of the N-terminal domain from Stayphlothermus marinus McrB (Sm3-180) at 1.92 Å, which adopts a PUA-like EVE fold that is closely related to the YTH and ASCH RNA binding domains. Unlike most PUA-like domains, Sm3-180 binds DNA and can associate with different modified substrates. We find the canonical 'aromatic cage' binding pocket that confers specificity for methylated bases in other EVE/YTH domains is degenerate and occluded in Sm3-180, which may contribute to its promiscuity in target recognition. Further structural comparison between different PUA-like domains identifies motifs and conformational variations that correlate with the preference for binding either DNA or RNA. Together these data have important implications for PUA-like domain specificity and suggest a broader biological versatility for the McrBC family than previously described.

PubMed: 32652237
DOI: 10.1016/j.jsb.2020.107572

Experimental method

X-RAY DIFFRACTION (1.92 Å)