7XM0

Crystal structure of Sau3AI-C and DNA substrate complex

Summary for 7XM0

• Entry DOI: 10.2210/pdb7xm0/pdb
• Descriptor: Type II restriction enzyme Sau3AI, DNA (5'-D(*CP*AP*TP*GP*AP*TP*CP*AP*TP*G)-3'), MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: sau3ai, restriction endonuclease, protein-dna complex, enzyme mechanism, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Staphylococcus aureus; More
• Total number of polymer chains: 9
• Total formula weight: 118541.76

Authors

Liu, Y.,Yu, F.,He, J. (deposition date: 2022-04-23, release date: 2023-04-26, Last modification date: 2024-11-06)

Primary citation

Liu, Y.,Xu, C.,Zhou, H.,Wang, W.,Liu, B.,Li, Y.,Hu, X.,Yu, F.,He, J.
The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism.
Structure, 31:1463-1472.e2, 2023

PubMed Abstract: The type II restriction endonuclease Sau3AI cleaves the sequence 5'-GATC-3' in double-strand DNA producing two sticky ends. Sau3AI cuts both DNA strands regardless of methylation status. Here, we report the crystal structures of the active site mutant Sau3AI-E64A and the C-terminal domain Sau3AI-C with a bound GATC substrate. Interestingly, the catalytic site of the N-terminal domain (Sau3AI-N) is spatially blocked by the C-terminal domain, suggesting a potential self-inhibition of the enzyme. Interruption of Sau3AI-C binding to substrate DNA disrupts Sau3AI function, suggesting a functional linkage between the N- and C-terminal domains. We propose that Sau3AI-C behaves as an allosteric effector binding one GATC substrate, which triggers a conformational change to open the N-terminal catalytic site, resulting in the subsequent GATC recognition by Sau3AI-N and cleavage of the second GATC site. Our data indicate that Sau3AI and UbaLAI might represent a new subclass of type IIE restriction enzymes.

PubMed: 37652002
DOI: 10.1016/j.str.2023.08.005

Experimental method

X-RAY DIFFRACTION (2.6 Å)