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TitleMechanistic and evolutionary insights into a type V-M CRISPR-Cas effector enzyme.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 8, Page 1172-1182, Year 2023
Publish dateJul 17, 2023
AuthorsSatoshi N Omura / Ryoya Nakagawa / Christian Südfeld / Ricardo Villegas Warren / Wen Y Wu / Hisato Hirano / Charlie Laffeber / Tsukasa Kusakizako / Yoshiaki Kise / Joyce H G Lebbink / Yuzuru Itoh / John van der Oost / Osamu Nureki /
PubMed AbstractRNA-guided type V CRISPR-Cas12 effectors provide adaptive immunity against mobile genetic elements (MGEs) in bacteria and archaea. Among diverse Cas12 enzymes, the recently identified Cas12m2 (CRISPR- ...RNA-guided type V CRISPR-Cas12 effectors provide adaptive immunity against mobile genetic elements (MGEs) in bacteria and archaea. Among diverse Cas12 enzymes, the recently identified Cas12m2 (CRISPR-Cas type V-M) is highly compact and has a unique RuvC active site. Although the non-canonical RuvC triad does not permit dsDNA cleavage, Cas12m2 still protects against invading MGEs through transcriptional silencing by strong DNA binding. However, the molecular mechanism of RNA-guided genome inactivation by Cas12m2 remains unknown. Here we report cryo-electron microscopy structures of two states of Cas12m2-CRISPR RNA (crRNA)-target DNA ternary complexes and the Cas12m2-crRNA binary complex, revealing structural dynamics during crRNA-target DNA heteroduplex formation. The structures indicate that the non-target DNA strand is tightly bound to a unique arginine-rich cluster in the recognition (REC) domains and the non-canonical active site in the RuvC domain, ensuring strong DNA-binding affinity of Cas12m2. Furthermore, a structural comparison of Cas12m2 with TnpB, a putative ancestor of Cas12 enzymes, suggests that the interaction of the characteristic coiled-coil REC2 insertion with the protospacer-adjacent motif-distal region of the heteroduplex is crucial for Cas12m2 to engage in adaptive immunity. Collectively, our findings improve mechanistic understanding of diverse type V CRISPR-Cas effectors and provide insights into the evolution of TnpB to Cas12 enzymes.
External linksNat Struct Mol Biol / PubMed:37460897 / PubMed Central
MethodsEM (single particle)
Resolution2.87 - 3.73 Å
Structure data

34803

8hhl

EMDB-34803, PDB-8hhl:
Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex
Method: EM (single particle) / Resolution: 2.87 Å

34804

8hhm

EMDB-34804, PDB-8hhm:
Cryo-EM structure of the Cas12m2-crRNA-target DNA ternary complex intermediate state
Method: EM (single particle) / Resolution: 3.08 Å

34824

8hio

EMDB-34824, PDB-8hio:
Cryo-EM structure of the Cas12m2-crRNA binary complex
Method: EM (single particle) / Resolution: 3.73 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

Source
  • mycolicibacterium mucogenicum (bacteria)
KeywordsRNA BINDING PROTEIN / CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX

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