6P74

OLD nuclease from Thermus Scotoductus

Summary for 6P74

• Entry DOI: 10.2210/pdb6p74/pdb
• Descriptor: Putative ATP-dependent endonuclease of the OLD family, PLATINUM (II) ION, SULFATE ION, ... (6 entities in total)
• Functional Keywords: abc atpase, nuclease, hydrolase
• Biological source: Thermus scotoductus
• Total number of polymer chains: 1
• Total formula weight: 61849.10

Authors

Chappie, J.S.,Schiltz, C.J. (deposition date: 2019-06-04, release date: 2020-01-29, Last modification date: 2024-03-13)

Primary citation

Schiltz, C.J.,Adams, M.C.,Chappie, J.S.
The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases.
Nucleic Acids Res., 48:2762-2776, 2020

PubMed Abstract: OLD family nucleases contain an N-terminal ATPase domain and a C-terminal Toprim domain. Homologs segregate into two classes based on primary sequence length and the presence/absence of a unique UvrD/PcrA/Rep-like helicase gene immediately downstream in the genome. Although we previously defined the catalytic machinery controlling Class 2 nuclease cleavage, degenerate conservation of the C-termini between classes precludes pinpointing the analogous residues in Class 1 enzymes by sequence alignment alone. Our Class 2 structures also provide no information on ATPase domain architecture and ATP hydrolysis. Here we present the full-length structure of the Class 1 OLD nuclease from Thermus scotoductus (Ts) at 2.20 Å resolution, which reveals a dimerization domain inserted into an N-terminal ABC ATPase fold and a C-terminal Toprim domain. Structural homology with genome maintenance proteins identifies conserved residues responsible for Ts OLD ATPase activity. Ts OLD lacks the C-terminal helical domain present in Class 2 OLD homologs yet preserves the spatial organization of the nuclease active site, arguing that OLD proteins use a conserved catalytic mechanism for DNA cleavage. We also demonstrate that mutants perturbing ATP hydrolysis or DNA cleavage in vitro impair P2 OLD-mediated killing of recBC-Escherichia coli hosts, indicating that both the ATPase and nuclease activities are required for OLD function in vivo.

PubMed: 32009148
DOI: 10.1093/nar/gkaa059

Experimental method

X-RAY DIFFRACTION (2.2 Å)