9cji

From Proteopedia

Cas12a:gRNA:DNA (Acidaminococcus sp.) with 0 RNA:DNA base pairs, structure 2

Structural highlights

9cji is a 4 chain structure with sequence from Acidaminococcus sp. BV3L6 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CS12A_ACISB CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTTN in this organism) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26422227). Has dsDNA endonuclease activity, results in staggered 4-base 5' overhangs 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). Non-target strand cleavage by the RuvC domain is probably a prerequisite of target strand cleavage by the Nuc domain (PubMed:27114038). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]^[1] ^[2]

Publication Abstract from PubMed

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize approximately 20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a-RNA-DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation.,Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA Nucleic Acids Res. 2024 Dec 19:gkae1192. doi: 10.1093/nar/gkae1192. PMID:39698811^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015 Oct 22;163(3):759-71. doi: 10.1016/j.cell.2015.09.038. Epub 2015 Sep, 25. PMID:26422227 doi:http://dx.doi.org/10.1016/j.cell.2015.09.038
↑ Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Cell. 2016 May 5;165(4):949-62. doi: 10.1016/j.cell.2016.04.003. Epub 2016 Apr, 21. PMID:27114038 doi:http://dx.doi.org/10.1016/j.cell.2016.04.003
↑ Soczek KM, Cofsky JC, Tuck OT, Shi H, Doudna JA. CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation. Nucleic Acids Res. 2024 Dec 19:gkae1192. PMID:39698811 doi:10.1093/nar/gkae1192