- EMDB-26959: Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarec... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-26959
タイトル
Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
マップデータ
70S ribosome with mRNA, P-site tRNA and Sarecycline bound
試料
複合体: 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
RNA: x 5種
タンパク質・ペプチド: x 49種
リガンド: x 4種
キーワード
ribosome / sarecycline / acne / ANTIBIOTIC
機能・相同性
機能・相同性情報
ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation ...ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein S14, type Z / Ribosomal protein L31 type A / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / : / : / Ribosomal protein L28 / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L20 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L34, conserved site / Ribosomal L28 family / Ribosomal protein L34 signature. / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L16 / : / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / L28p-like / Ribosomal protein L20 / Ribosomal protein S15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 類似検索 - ドメイン・相同性
50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 30S ribosomal protein S10 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 ...50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L24 / 30S ribosomal protein S10 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS13 / 50S ribosomal protein L35 / Large ribosomal subunit protein uL5 / AURKAIP1/COX24 domain-containing protein 類似検索 - 構成要素
ジャーナル: Nucleic Acids Res / 年: 2023 タイトル: Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. 著者: Ivan B Lomakin / Swapnil C Devarkar / Shivali Patel / Ayman Grada / Christopher G Bunick / 要旨: Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, ...Acne vulgaris is a chronic disfiguring skin disease affecting ∼1 billion people worldwide, often having persistent negative effects on physical and mental health. The Gram-positive anaerobe, Cutibacterium acnes is implicated in acne pathogenesis and is, therefore, a main target for antibiotic-based acne therapy. We determined a 2.8-Å resolution structure of the 70S ribosome of Cutibacterium acnes by cryogenic electron microscopy and discovered that sarecycline, a narrow-spectrum antibiotic against Cutibacterium acnes, may inhibit two active sites of this bacterium's ribosome in contrast to the one site detected previously on the model ribosome of Thermus thermophilus. Apart from the canonical binding site at the mRNA decoding center, the second binding site for sarecycline exists at the nascent peptide exit tunnel, reminiscent of the macrolides class of antibiotics. The structure also revealed Cutibacterium acnes-specific features of the ribosomal RNA and proteins. Unlike the ribosome of the Gram-negative bacterium Escherichia coli, Cutibacterium acnes ribosome has two additional proteins, bS22 and bL37, which are also present in the ribosomes of Mycobacterium smegmatis and Mycobacterium tuberculosis. We show that bS22 and bL37 have antimicrobial properties and may be involved in maintaining the healthy homeostasis of the human skin microbiome.