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

M. Cemre Manav, Lan B. Van, Jinzhong Lin, Anders Fuglsang, Xu Peng () and Ditlev E. Brodersen ()
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M. Cemre Manav: Aarhus University
Lan B. Van: Aarhus University
Jinzhong Lin: University of Copenhagen
Anders Fuglsang: University of Copenhagen
Xu Peng: University of Copenhagen
Ditlev E. Brodersen: Aarhus University

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-19847-x

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