Structural basis for inhibition of an archaeal CRISPR–Cas type I-D large subunit by an anti-CRISPR protein

• Published in: Nature communications Vol. 11; no. 1; p. 5993
• Main Authors: Manav, M. Cemre, Van, Lan B., Lin, Jinzhong, Fuglsang, Anders, Peng, Xu, Brodersen, Ditlev E.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.11.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/326/4041; 631/45/147; 631/535/1266; Archaeal Proteins - antagonists & inhibitors; Archaeal Proteins - metabolism; Archaeal Proteins - ultrastructure; Cleavage; CRISPR; CRISPR-Associated Proteins - antagonists & inhibitors; CRISPR-Associated Proteins - metabolism; CRISPR-Associated Proteins - ultrastructure; CRISPR-Cas Systems - genetics; Crystal structure; DNA Cleavage; DNA helicase; Domains; Histidine; Host-Pathogen Interactions - genetics; Humanities and Social Sciences; multidisciplinary; Nuclease; Phages; Protein A; Protein Domains - genetics; Proteins; Repressor Proteins - genetics; Repressor Proteins - metabolism; Rudiviridae - genetics; Rudiviridae - metabolism; Rudiviridae - pathogenicity; Science; Science (multidisciplinary); Sulfolobus; Sulfolobus - genetics; Sulfolobus - virology; Viral Proteins - genetics; Viral Proteins - metabolism; Viral Proteins - ultrastructure; Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-19847-x

A hallmark of type I CRISPR–Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3’ subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR–Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence. In type I-D CRISPR–Cas systems, the nuclease and helicase activities are carried out by separate subunits. The crystal structure of Sulfolobus islandicus type I-D large subunit Cas10d, containing a nuclease domain, reveals unusual architecture. The structure of Cas10d in complex with anti-CRISPR protein AcrID1 suggests that the latter sequesters Cas10d in a nonfunctional state.