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Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z. The crystal structure of Cpf1 in complex with CRISPR RNA. Nature 2016; 532:522-6. [PMID: 27096363 DOI: 10.1038/nature17944] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/29/2016] [Indexed: 12/13/2022]
Abstract
The CRISPR-Cas systems, as exemplified by CRISPR-Cas9, are RNA-guided adaptive immune systems used by bacteria and archaea to defend against viral infection. The CRISPR-Cpf1 system, a new class 2 CRISPR-Cas system, mediates robust DNA interference in human cells. Although functionally conserved, Cpf1 and Cas9 differ in many aspects including their guide RNAs and substrate specificity. Here we report the 2.38 Å crystal structure of the CRISPR RNA (crRNA)-bound Lachnospiraceae bacterium ND2006 Cpf1 (LbCpf1). LbCpf1 has a triangle-shaped architecture with a large positively charged channel at the centre. Recognized by the oligonucleotide-binding domain of LbCpf1, the crRNA adopts a highly distorted conformation stabilized by extensive intramolecular interactions and the (Mg(H2O)6)(2+) ion. The oligonucleotide-binding domain also harbours a looped-out helical domain that is important for LbCpf1 substrate binding. Binding of crRNA or crRNA lacking the guide sequence induces marked conformational changes but no oligomerization of LbCpf1. Our study reveals the crRNA recognition mechanism and provides insight into crRNA-guided substrate binding of LbCpf1, establishing a framework for engineering LbCpf1 to improve its efficiency and specificity for genome editing.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats/genetics
- Crystallography, X-Ray
- Firmicutes/enzymology
- Genetic Engineering
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Structure, Tertiary
- RNA Stability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Substrate Specificity
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Affiliation(s)
- De Dong
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Kuan Ren
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Xiaolin Qiu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Jianlin Zheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Minghui Guo
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Xiaoyu Guan
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Hongnan Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Ningning Li
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bailing Zhang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Daijun Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Chuang Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Shuo Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Dan Wu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Yunfeng Ma
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Shilong Fan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhiwei Huang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
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Abstract
The site-specific recombinase encoded by bacteriophage λ (Int) is responsible for integrating and excising the viral chromosome into and out of the chromosome of its Escherichia coli host. Int carries out a reaction that is highly directional, tightly regulated, and depends upon an ensemble of accessory DNA bending proteins acting on 240 bp of DNA encoding 16 protein binding sites. This additional complexity enables two pathways, integrative and excisive recombination, whose opposite, and effectively irreversible, directions are dictated by different physiological and environmental signals. Int recombinase is a heterobivalent DNA binding protein and each of the four Int protomers, within a multiprotein 400 kDa recombinogenic complex, is thought to bind and, with the aid of DNA bending proteins, bridge one arm- and one core-type DNA site. In the 12 years since the publication of the last review focused solely on the λ site-specific recombination pathway in Mobile DNA II, there has been a great deal of progress in elucidating the molecular details of this pathway. The most dramatic advances in our understanding of the reaction have been in the area of X-ray crystallography where protein-DNA structures have now been determined for of all of the DNA-protein interfaces driving the Int pathway. Building on this foundation of structures, it has been possible to derive models for the assembly of components that determine the regulatory apparatus in the P-arm, and for the overall architectures that define excisive and integrative recombinogenic complexes. The most fundamental additional mechanistic insights derive from the application of hexapeptide inhibitors and single molecule kinetics.
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The carboxy-terminal αN helix of the archaeal XerA tyrosine recombinase is a molecular switch to control site-specific recombination. PLoS One 2013; 8:e63010. [PMID: 23667562 PMCID: PMC3646895 DOI: 10.1371/journal.pone.0063010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/27/2013] [Indexed: 11/21/2022] Open
Abstract
Tyrosine recombinases are conserved in the three kingdoms of life. Here we present the first crystal structure of a full-length archaeal tyrosine recombinase, XerA from Pyrococcus abyssi, at 3.0 Å resolution. In the absence of DNA substrate XerA crystallizes as a dimer where each monomer displays a tertiary structure similar to that of DNA-bound Tyr-recombinases. Active sites are assembled in the absence of dif except for the catalytic Tyr, which is extruded and located equidistant from each active site within the dimer. Using XerA active site mutants we demonstrate that XerA follows the classical cis-cleavage reaction, suggesting rearrangements of the C-terminal domain upon DNA binding. Surprisingly, XerA C-terminal αN helices dock in cis in a groove that, in bacterial tyrosine recombinases, accommodates in trans αN helices of neighbour monomers in the Holliday junction intermediates. Deletion of the XerA C-terminal αN helix does not impair cleavage of suicide substrates but prevents recombination catalysis. We propose that the enzymatic cycle of XerA involves the switch of the αN helix from cis to trans packing, leading to (i) repositioning of the catalytic Tyr in the active site in cis and (ii) dimer stabilisation via αN contacts in trans between monomers.
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