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  1. Article ; Online: Lateral access mechanism of LPA receptor probed by molecular dynamics simulation.

    Rieko Suenaga / Mizuki Takemoto / Asuka Inoue / Ryuichiro Ishitani / Osamu Nureki

    PLoS ONE, Vol 17, Iss 2, p e

    2022  Volume 0263296

    Abstract: G-protein-coupled receptors (GPCR) are a family of membrane receptors that play important roles in the regulation of various physiological phenomena. LPA receptors (LPA1-6) are members of the class A GPCRs, which transduce a lysophosphatidic acid (LPA) ... ...

    Abstract G-protein-coupled receptors (GPCR) are a family of membrane receptors that play important roles in the regulation of various physiological phenomena. LPA receptors (LPA1-6) are members of the class A GPCRs, which transduce a lysophosphatidic acid (LPA) signal across the cell membrane and evoke various responses, including cellular survival, proliferation, differentiation, and migration. The crystal structure of LPA6 revealed a gap between its transmembrane helices (TMs), which is opened toward the membrane side. This led to the proposal of the "lateral access model," in which its lipophilic ligand directly enters the binding pocket through the gap structure at the membrane. In this study, we performed molecular dynamics (MD) simulations and Markov state model (MSM) analyses of LPA6 and LPA, to elucidate the long timescale dynamics of the ligand binding process. The results from the 71.4-μs MD simulation suggested that the flexibility of the TMs constituting the gap structure enables the lateral entrance of the ligand, and the key interactions between the receptor and ligand facilitate the transition state of the ligand binding process.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9

    Hirano, Seiichi / Hiroshi Nishimasu / Osamu Nureki / Ryuichiro Ishitani

    Molecular cell. 2016 Mar. 17, v. 61, no. 6

    2016  

    Abstract: The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets bearing a PAM (protospacer adjacent motif) and complementarity to the guide RNA. A recent study showed that, whereas wild-type Streptococcus pyogenes Cas9 (SpCas9) recognizes the 5′-NGG- ...

    Abstract The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets bearing a PAM (protospacer adjacent motif) and complementarity to the guide RNA. A recent study showed that, whereas wild-type Streptococcus pyogenes Cas9 (SpCas9) recognizes the 5′-NGG-3′ PAM, the engineered VQR, EQR, and VRER SpCas9 variants recognize the 5′-NGA-3′, 5′-NGAG-3′, and 5′-NGCG-3′ PAMs, respectively, thus expanding the targetable sequences in Cas9-mediated genome editing applications. Here, we present the high-resolution crystal structures of the three SpCas9 variants in complexes with a single-guide RNA and its altered PAM-containing, partially double-stranded DNA targets. A structural comparison of the three SpCas9 variants with wild-type SpCas9 revealed that the multiple mutations synergistically induce an unexpected displacement in the phosphodiester backbone of the PAM duplex, thereby allowing the SpCas9 variants to directly recognize the altered PAM nucleotides. Our findings explain the altered PAM specificities of the SpCas9 variants and establish a framework for further rational engineering of CRISPR-Cas9.
    Keywords crystal structure ; DNA ; engineering ; genome ; mutation ; nucleotides ; RNA ; Streptococcus pyogenes
    Language English
    Dates of publication 2016-0317
    Size p. 886-894.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2016.02.018
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9

    Seiichi Hirano / Omar O. Abudayyeh / Jonathan S. Gootenberg / Takuro Horii / Ryuichiro Ishitani / Izuho Hatada / Feng Zhang / Hiroshi Nishimasu / Osamu Nureki

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: The RNA-guided DNA endonuclease Cas9 from Corynebacterium diphtheriae (CdCas9) recognizes a promiscuous protospacer adjacent motif (PAM). Here the authors provide insights into the CdCas9-mediated PAM recognition mechanism by determining the 2.9 Å ... ...

    Abstract The RNA-guided DNA endonuclease Cas9 from Corynebacterium diphtheriae (CdCas9) recognizes a promiscuous protospacer adjacent motif (PAM). Here the authors provide insights into the CdCas9-mediated PAM recognition mechanism by determining the 2.9 Å crystal structure of CdCas9 in complex with the guide RNA and its target DNA, which is of interest for engineering of CRISPR-Cas9 genome-editor nucleases.
    Keywords Science ; Q
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9

    Seiichi Hirano / Omar O. Abudayyeh / Jonathan S. Gootenberg / Takuro Horii / Ryuichiro Ishitani / Izuho Hatada / Feng Zhang / Hiroshi Nishimasu / Osamu Nureki

    Nature Communications, Vol 10, Iss 1, Pp 1-

    2019  Volume 11

    Abstract: The RNA-guided DNA endonuclease Cas9 from Corynebacterium diphtheriae (CdCas9) recognizes a promiscuous protospacer adjacent motif (PAM). Here the authors provide insights into the CdCas9-mediated PAM recognition mechanism by determining the 2.9 Å ... ...

    Abstract The RNA-guided DNA endonuclease Cas9 from Corynebacterium diphtheriae (CdCas9) recognizes a promiscuous protospacer adjacent motif (PAM). Here the authors provide insights into the CdCas9-mediated PAM recognition mechanism by determining the 2.9 Å crystal structure of CdCas9 in complex with the guide RNA and its target DNA, which is of interest for engineering of CRISPR-Cas9 genome-editor nucleases.
    Keywords Science ; Q
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1

    Nishimasu, Hiroshi / Feng Zhang / Linyi Gao / Osamu Nureki / Ryuichiro Ishitani / Takashi Yamano

    Molecular cell. 2017 July 06, v. 67, no. 1

    2017  

    Abstract: The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA ... ...

    Abstract The RNA-guided Cpf1 nuclease cleaves double-stranded DNA targets complementary to the CRISPR RNA (crRNA), and it has been harnessed for genome editing technologies. Recently, Acidaminococcus sp. BV3L6 (AsCpf1) was engineered to recognize altered DNA sequences as the protospacer adjacent motif (PAM), thereby expanding the target range of Cpf1-mediated genome editing. Whereas wild-type AsCpf1 recognizes the TTTV PAM, the RVR (S542R/K548V/N552R) and RR (S542R/K607R) variants can efficiently recognize the TATV and TYCV PAMs, respectively. However, their PAM recognition mechanisms remained unknown. Here we present the 2.0 Å resolution crystal structures of the RVR and RR variants bound to a crRNA and its target DNA. The structures revealed that the RVR and RR variants primarily recognize the PAM-complementary nucleotides via the substituted residues. Our high-resolution structures delineated the altered PAM recognition mechanisms of the AsCpf1 variants, providing a basis for the further engineering of CRISPR-Cpf1.
    Keywords Acidaminococcus ; crystal structure ; DNA ; engineering ; gene editing ; nucleotide sequences ; nucleotides ; RNA
    Language English
    Dates of publication 2017-0706
    Size p. 139-147.e2.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2017.04.019
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  6. Article: Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1

    Yamano, Takashi / Bernd Zetsche / Feng Zhang / Hiroshi Nishimasu / Osamu Nureki / Ryuichiro Ishitani

    Molecular cell. 2017 Aug. 17, v. 67, no. 4

    2017  

    Abstract: The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium ( ... ...

    Abstract The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.
    Keywords Acidaminococcus ; bacteria ; crystal structure ; DNA ; DNA damage ; gene editing ; Lachnospiraceae ; nucleases ; nucleotide sequences ; RNA
    Language English
    Dates of publication 2017-0817
    Size p. 633-645.e3.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2017.06.035
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1

    Kazuki Kato / Hiroshi Nishimasu / Daisuke Oikawa / Seiichi Hirano / Hisato Hirano / Go Kasuya / Ryuichiro Ishitani / Fuminori Tokunaga / Osamu Nureki

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 8

    Abstract: Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP ... ...

    Abstract Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG and discuss mechanistic implications.
    Keywords Science ; Q
    Language English
    Publishing date 2018-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1

    Kazuki Kato / Hiroshi Nishimasu / Daisuke Oikawa / Seiichi Hirano / Hisato Hirano / Go Kasuya / Ryuichiro Ishitani / Fuminori Tokunaga / Osamu Nureki

    Nature Communications, Vol 9, Iss 1, Pp 1-

    2018  Volume 8

    Abstract: Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP ... ...

    Abstract Ecto-nucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) is a type II transmembrane glycoprotein that hydrolyzes both ATP and cGAMP. Here the authors present the crystal structures of the extracellular domain of mouse ENPP1 in complex with 3′3′-cGAMP and the reaction intermediate pA(3′,5′)pG and discuss mechanistic implications.
    Keywords Science ; Q
    Language English
    Publishing date 2018-10-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article: Vibrational and Molecular Properties of Mg²⁺ Binding and Ion Selectivity in the Magnesium Channel MgtE

    Kimura, Tetsunari / Victor A. Lorenz-Fonfria / Shintaro Douki / Hideyoshi Motoki / Ryuichiro Ishitani / Osamu Nureki / Masahiro Higashi / Yuji Furutani

    Journal of physical chemistry. 2018 Sept. 25, v. 122, no. 42

    2018  

    Abstract: Magnesium ions (Mg²⁺) are crucial for various biological processes. A bacterial Mg²⁺ channel, MgtE, tightly regulates the intracellular Mg²⁺ concentration. Previous X-ray crystal structures showed that MgtE forms a dimeric structure composed of a total ... ...

    Abstract Magnesium ions (Mg²⁺) are crucial for various biological processes. A bacterial Mg²⁺ channel, MgtE, tightly regulates the intracellular Mg²⁺ concentration. Previous X-ray crystal structures showed that MgtE forms a dimeric structure composed of a total of 10 transmembrane α helices forming a central pore, and intracellular soluble domains constituting a Mg²⁺ sensor. The ion selectivity for Mg²⁺ over Ca²⁺ resides at a central cavity in the transmembrane pore of MgtE, involving a conserved aspartate residue (Asp432) from each monomer. Here, we applied ion-exchange-induced difference FTIR spectroscopy to analyze the interactions between MgtE and divalent cations, Mg²⁺ and Ca²⁺. Using site-directed mutagenesis, vibrational bands at 1421 (Mg²⁺), 1407 (Mg²⁺), ∼1440 (Ca²⁺), and 1390 (Ca²⁺) cm–¹ were assigned to symmetric carboxylate stretching modes of Asp432, involved in the ion coordination. Conservative modifications of the central cavity by Asp432Glu or Ala417Leu mutations resulted in the disappearance of the Mg²⁺-sensitive carboxylate bands, suggesting a highly optimized geometry for accommodating a Mg²⁺ ion. The dependency of the vibrational changes on Mg²⁺ and Ca²⁺ concentrations revealed the presence of a two different classes of binding sites: a high affinity site for Mg²⁺ (Kd ≈ 0.3 mM) with low Ca²⁺ affinity (Kd ≈ 80 mM), and a medium affinity site for Mg²⁺ (Kd ≈ 2 mM) and Ca²⁺ (Kd ≈ 6 mM), tentatively assigned to the central cavity and the sensor domain, respectively. With the aid of molecular dynamics simulation and normal-mode analysis by quantum chemistry, we confirm that changes in carboxylate bands of the high affinity binding site originate from Asp432 in the central cavity.
    Keywords Fourier transform infrared spectroscopy ; aspartic acid ; binding sites ; calcium ; cations ; crystal structure ; magnesium ; molecular dynamics ; site-directed mutagenesis
    Language English
    Dates of publication 2018-0925
    Size p. 9681-9696.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021/acs.jpcb.8b07967
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  10. Article ; Online: Crystal structure of Drosophila Piwi

    Sonomi Yamaguchi / Akira Oe / Kazumichi M. Nishida / Keitaro Yamashita / Asako Kajiya / Seiichi Hirano / Naoki Matsumoto / Naoshi Dohmae / Ryuichiro Ishitani / Kuniaki Saito / Haruhiko Siomi / Hiroshi Nishimasu / Mikiko C. Siomi / Osamu Nureki

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 13

    Abstract: PIWI-clade Argonautes bind PIWI-interacting RNAs (piRNAs) to silence transposons and maintain genome integrity in animal gonads. Here the authors present the crystal structure of a Drosophila Piwi–piRNA complex isolated from cultured fly ovarian somatic ... ...

    Abstract PIWI-clade Argonautes bind PIWI-interacting RNAs (piRNAs) to silence transposons and maintain genome integrity in animal gonads. Here the authors present the crystal structure of a Drosophila Piwi–piRNA complex isolated from cultured fly ovarian somatic cells and find that it contains a non-canonical DVDK tetrad, and lacks slicer activity in vitro.
    Keywords Science ; Q
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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